RAx ML New Manual
User Manual:
Open the PDF directly: View PDF 
.
Page Count: 61
!"
"#$%&
"!
'(
)*'+
, -.
, /(
, ,0 "
, (11
, (
2(1
/(/ /
(
("
134
I. About RAxML
56 7 ( ! 3 (
!"!(" " ! (*
!!("8!8("!
!!-9." . ! :1;
."(!<= <("
When using RAxML please cite:
> ? , > ! <" <* !
<? 8 $%@8 ( "" >
(>AA!"!BA"AA$%@A$%A%A!"$##"C
(D!0BD,E3+:=/-"!$<
II. Getting help
(( ( ' ( > (>AA("A!AC
DFG!A98'("!"G
8!((>
% "(!"G
!H.(8IG
# (""J=H"
!
Do never send emails with RAxML questions to A. Stamatakis directly!
1
( ( . " " > (>AA"*
AA.A!.AAK
(88("("!.
(>(>AA"*AA.A!.AA
III. RAxML web-servers and Graphical User Interfaces
) .* . 8 "
!
% /(<.>(>AA...(AK"A(A
.* .6>(>AA*"A*A
# "!E<">(>AA(*A
L"("!"((8'+ (
" " 1!8 ." >
(>AA"!A(B"AA
98 .( !((! '+ 8 ""
!
IV. Downloading RAxML
( " '9+ '< (>
(>AA"AA*."..(
watch((""
)(((.!(!"G
,!. x.y.z . x ".B"68 y
"..!z".I
V. Compiling RAxML
"!MN
"38(< 5(!"7<!
*"
A"<O< (6< (
("("M".
<(6""!")""
5< 7I*5<7(
8!"(..!"
8< (AM!!"8"
""("G
("("(.("""
G&("(.!"*"""G
2
-(..(".((E#""88!.
!,!,"""
""("(""
8."(".("(!
/<+5798((%/<+A"8".(
.."(<!
9.H""8...I">
standard-RAxML-8.0.0.tar.gz
"((>
gunzip standard-RAxML-8.0.0.tar.gz
tar xf standard-RAxML-8.0.0.tar
""""I">
cd standard-RAxML-8.0.0/
ls
""usefulScripts""(!("(!
98HI>
ls Makefile.*
.".>
I!38< A<83!/
""(8< 8<8<!/"
","">
Makefile.AVX2.gcc
Makefile.AVX2.HYBRID.gcc
Makefile.AVX2.mac
Makefile.AVX2.MPI.gcc
Makefile.AVX2.PTHREADS.gcc
Makefile.AVX2.PTHREADS.mac
/(I,">
Makefile.AVX.gcc
Makefile.AVX.HYBRID.gcc
Makefile.AVX.mac
Makefile.AVX.MPI.gcc
Makefile.AVX.PTHREADS.gcc
Makefile.AVX.PTHREADS.mac
/(I""53./<+
P*& G7 I "> Makefile.QuartetMPI.gcc " I
(< (6!3!"8!"
""G
3
Makefile.gcc
Makefile.HYBRID.gcc
Makefile.MPI.gcc
Makefile.PTHREADS.gcc
Makefile.PTHREADS.mac
Makefile.QuartetMPI.gcc
/(IE#">
Makefile.SSE3.gcc
Makefile.SSE3.HYBRID.gcc
Makefile.SSE3.mac
Makefile.SSE3.MPI.gcc
Makefile.SSE3.PTHREADS.gcc
Makefile.SSE3.PTHREADS.mac
Makefile.SSE3.QuartetMPI.gcc
9."(((,"8"(3(>
make -f Makefile.AVX.gcc
."">
raxmlHPC-AVX
9.8"(<8IB"I"(
3(>
rm *.o
(>
make -f Makefile.AVX.PTHREADS.gcc
.".""
raxmlHPC-PTHREADS-AVX
/((N8.L"<
(""8< "("< "((2(<
+8!"
! 3 ! !
(((("(
< . . . ! 8 (!"
.*(G
.8 ! 5%8Q$$ 8 %8$$(8 -9 7 .
((!!"&P*"
1 5%P 8 $8$$$ *(8 -97 . I" (*
((!%$*%%*"
Warning>("!"!/<+ -T
( ! " 8 . I"
4
(!""G
< !"("5%$$%8$$$(7
"="(!(!"(I*
.!
18(R""(6.<
Warning:"!"!< G"< .((!
("! -# -N ( " 8 " (
!"(AR5(7"(G
1(8!(!"*("
G
(("!.<!(I.
( A(! (" L ! ) *
*""("L!8!"8@@*./<+
@""./<+88thread0 CPU08
thread1CPU1"
(!L""8"""""*!8."
.(!("8/<+ !
8!"8thread0"CPU0CPU4"""
!/<+.*I)("L
8(!"(!PS L"
*
!" ." (/<+88!" L8
9+A+9 R"!""""
"( ( ! 8 .
"N>
#define _PORTABLE_PTHREADS
axml.c"I
!"
(.(L""!<!(
98.("(( "!
"!"A(".8"
("8""(.!(
( "" ." "( ""(.
H.5(>AA.(A.AHK.7
8!.#!%."
"#!8"". 8(
L""8 8 . . A" " " L" (
(8("!"(
( RAxML_info.runIDI
>
Alignment has 70 distinct alignment patterns
! H"A(P$$-9(88!8H
(B3*-9.%$$$
"6.@8(8
5
A""L"
8L""((!8("8!
58@-98$!(78!.
((A"!"L"("
"(.5"(7((
!")(3(!
L"8.%$$$((L".%&
"A
18(L""()'
"("("./
"((T!"('3
98B!8.(!
G
VI. RAxML Likelihood Values & Idiosyncrasies
( (" ""
"(!(.8!"
(.("(!
5.UAV%$!<=' 7
!"!"8!"
( . M ( " M "
.
98.<=A' "
"' M(""(("!3"
5-"J."8(""87."
(<=
.A<=' ((
*8M
8("""(."
!3"""!"(
((6("G
8!."(("(.("
8(6"(!I(
.(
"("(5-f e788"(
(<=5(>AA..."*(!A(A7
#$%&
(("!"
"!I(
.8!.("!" I"..
E!."3"5!""(8."
7!(((N((""
"(..(M
( M" I . ' 8
4<99 8<=85(.M7
6
="(.""(6N-O2!
I ."."8"3
(6"8.M"8*N(
(
(((""5!(67"
("" I
E(" . %8$$$ 3" M" "
"(8((6.
( 5 -e (7 ! % 8 8 ! M" ( . .
""((6%$.((68
.".M"
98!(!(;."
.8"(((
! " ! "! " /
(<R5(>AA""A<(AA...A7
+!8 ..!. "/8/
"( MG .8 " " !
"."(".(...(("(
Warning: /((!
.P$ .("
(*(
/"""(.G<
("((
(>AA(A(AB(C(D0D%&#QP#P0D(S#S1
S1(S1(S1KB(S#1S#-%&#QP#P
./.8."5""(M!
""!'78.!
GTRCAT (( "( .W ! . '
!"' !/
((8 8 "" " "(
!((".GTRCAT. ;GTRGAMMA(!"
!'
GTRCAT .!!("
I" . "( " 5 @ !7
"(5@.7
E8 GTRCAT ( *" '& ( ((" (
(!("8.".GTRGAMMA
.8.(6"GTRCAT8
"(GTRCAT"(
Warning:"((/*"G
=.(! . GTRCAT "
7
((!((/((..
(((
8/((!...
P$!"""""
.8! "/'.
3 . ! " ' .
"("8'.!".
%$8$$$5(>AA...""A%@X%*%$PA%A@X$7
! /* "" 1* ((8
(>AA...(A"A!>S1%$%#X%S1B($$$Q@Q$
VII. Alignment input File Formats
(")
Alignments:(!!3<= <
1 *+ 3" " ! . % ( P&
""
!"("#define nmlngth 256"
Iaxml.h(((
8 . (" <= < ! 58 8 "7 !
<= <I
Trees:(!9."8(."(8
8"!
(>AA".A((A." ! 9."
!
&
"" ! !. AL"" !
.("!"(
"6""!!.>
% " 3" 57 (( ( 8 "
(( . ( <= < I ! ." "
3"%$""
" 3"57 M " "
((."**!
# +/57 """.
8""!X, ?, *, -!N, O, X, ?,
-!-95!(7
@ +3"57"""57.
</"57"!!.("""8
88"8.!!.("">:
() []
8
"""3"A"."8
8 . -n alignmentName . " . I "
alignmentName.reduced ."3"A"
!"!(("ImodelFileName.reduced
. . " " " 3"
3"""...I
VIII. The RAxML options
!("((((
!3" " !. ..
B3"6"88</"
.""((((!
8*((>
raxmlHPC -h
.!.88.".>
raxmlHPC -s sequenceFileName -n outputFileName -m substitutionModel
[-a weightFileName] [-A secondaryStructureSubstModel]
[-b bootstrapRandomNumberSeed] [-B wcCriterionThreshold]
[-c numberOfCategories] [-C] [-d] [-D]
[-e likelihoodEpsilon] [-E excludeFileName]
[-f a|A|b|B|c|C|d|D|e|E|F|g|G|h|H|i|I|j|J|k|m|n|N|o|p|q|r|R|s|S|t|T|u|
v|V|w|W|x|y]
[-F]
[-g groupingFileName] [-G placementThreshold] [-h] [-H]
[-i initialRearrangementSetting]
[-I autoFC|autoMR|autoMRE|autoMRE_IGN]
[-j] [-J MR|MR_DROP|MRE|STRICT|STRICT_DROP|T_<PERCENT>] [-k] [-K]
[-L MR|MRE|T_<PERCENT>] [-M]
[-o outGroupName1[,outGroupName2[,...]]][-O]
[-p parsimonyRandomSeed] [-P proteinModel]
[-q multipleModelFileName] [-r binaryConstraintTree]
[-R binaryModelParamFile] [-S secondaryStructureFile]
[-t userStartingTree]
[-T numberOfThreads] [-u] [-U] [-v] [-V] [-w outputDirectory]
[-W slidingWindowSize]
[-x rapidBootstrapRandomNumberSeed][-X][-y]
[-Y quartetGroupingFileName|ancestralSequenceCandidatesFileName]
[-z multipleTreesFile]
[-#|-N numberOfRuns|autoFC|autoMR|autoMRE|autoMRE_IGN]
[--mesquite][--silent][--no-seq-check][--no-bfgs]
[--asc-corr=stamatakis|felsenstein|lewis]
[--flag-check]
[--auto-prot=ml|bic|aic|aicc ]
[--epa-keep-placements=number]
[--epa-accumulated-threshold=threshold]
[--epa-prob-threshold=threshold]
9
[--JC69][--K80]
[--set-thread-affinity]
[--bootstop-perms=number]
[--quartets-without-replacement]
-a Specify a column weight file name to assign individual weights to each
column of the alignment. Those weights must be integers separated by any
type and number of white-spaces within a separate file.
8 ! " . "
"!(.I">
5 1 1 2 1 1 1 1 1 1 1 2 1 1 3 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 4 1 1 1 4 1 1
Example:raxmlHPC -a wgtFile -s alg.phy -p 12345 -m GTRCAT -n TEST
-A Specify one of the secondary structure substitution models implemented in
RAxML. The same nomenclature as in the PHASE manual is used, available
models: S6A, S6B, S6C, S6D, S6E, S7A, S7B, S7C, S7D, S7E, S7F, S16, S16A,
S16B
DEFAULT: 16-state GTR model (S16)
98(.."""
""(((8!"
("!II""-S(
Example:raxmlHPC -S secondaryStructureFile -s alg.phy -A S7D -p 12345 -m
GTRGAMMA -n TEST
-b Specify an integer number (random seed) and turn on bootstrapping
DEFAULT: OFF
(.*("((.!("
!3(8("!88
-b 123476
9.8((. ( </*<
("(!"("!
Example:raxmlHPC -b 12345 -p 12345 -# 100 -s alg -m GTRCAT -n TEST
-B specify a floating point number between 0.0 and 1.0 that will be used as
cutoff threshold for the MR-based bootstopping criteria. The recommended
setting is 0.03.
DEFAULT: 0.03 (recommended empirically determined setting)
.("!!*"((".
"!""((""!
(( 9 8 M" !
(("B"!
""(.M".W"W!3"
(( " < " "( ((>
(>AA("A"(A%$%$$XAQX*#*&@*$$$*XK%#F(*%
10
Example:raxmlHPC -B 0.02 -b 12345 -p 12345 -# AUTOMR -s alg -m GTRCAT -n
TEST
-c Specify number of distinct rate categories for RAxML when model of rate
heterogeneity is set to CAT.
Individual per-site rates are categorized into numberOfCategories rate
categories to accelerate computations.
DEFAULT: 25
Example:raxmlHPC -c 40 -p 12345 -s alg -m GTRCAT -n TEST
Warning: Note that the setting of -c has no eect whatsoever on the number of discrete rate
categories that are used to approximate the Gamma distribution of rate heterogeneity!
RAxML always uses 4 discrete rate categories to approximate Gamma!
-C Enable verbose output for the "-L" and "-f i" options. This will produce
more, as well as more verbose output files
DEFAULT: OFF
(.((I.
"( / / " " >
(>AA..."AABA@QXAX@@QA!A%%#$
"!.(( .."
>
(>AA!BA"AA$%@A$A$XA$&%" (D
!0BD &P1'9$62.
Example: raxmlHPC -L -m GTRCAT -L MRE -z treeSet -n TEST
-d start ML optimization from random starting tree
DEFAULT: OFF
(."."(
!!6(.<2
5%$$W$$7
(!"".""(("
("
8WW
!!("("
G
Example: raxmlHPC -d -p 12345 -s alg -m GTRGAMMA -n TEST
-D ML search convergence criterion. This will break off ML searches if the
relative Robinson-Foulds distance between the trees obtained from two
consecutive lazy SPR cycles is smaller or equal to 1%. Usage recommended for
very large datasets in terms of taxa.
On trees with more than 500 taxa this will yield execution time improvements
of approximately 50% while yielding only slightly worse trees.
DEFAULT: OFF
11
)(8.(8.("8
. 1 " . . "" "" ! <
5<*'!7%S(
(.""(
"!.
"(>
> ?<" " ! ?
E8 = J8 /( R> "38
(("(("8P@X*PXX8:)8$%%
Example: raxmlHPC -D -p 12345 -s alg -m GTRCAT -n TEST
-e set model optimization precision in log likelihood units for final
optimization of tree topology
DEFAULT: 0.1 for models not using proportion of invariant sites estimate
0.001 for models using proportion of invariant sites estimate
.("!(."M"8(.
(6.'!.B
.-f e("!. -f n((
.!3"!"!I!
%8$$$"."!
(" -e 1.0 -e 2.0 ( "( " I
(
98(*(*M"("!%$$
!$%."(
L"("""
Example: raxmlHPC -f e -e 0.00001 -s alg -t tree -m GTRGAMMA -n TEST
-E specify an exclude file name, that contains a specification of alignment
positions you wish to exclude.
Format is similar to Nexus, the file shall contain entries like "100-200
300-400", to exclude a single column write, e.g., "100-100", if you specify
a partition file via “-q”, an appropriately adapted partition file will also
be written.
( . B . " I . "
""3!".""
!(8 ((( ( I. .
98".two-step("=.I
"-E(<= <!I.
".I..
5"alg.excludeFile(.7""8!"
Example: raxmlHPC -E excludeFile -s alg -m GTRCAT -q part -n TEST
"I."".alg.excludeFile
(I.("I"""part.excludeFile
!."%$$*%QQ5888%$$%QQ
".7$$*QQ"("IW(
IW."..>
12
100-199
200-299
-f select algorithm:
*!((.!("8"8.".
!" !H("!-f."
"5-f d(7(.
-f a rapid Bootstrap analysis and search for best-scoring ML tree in one program
run
""(R("!*"
(
Example: raxmlHPC -f a -p 12345 -s alg -x 12345 -# 100 -m GTRCAT -n TEST
-f A compute marginal ancestral states on a ROOTED reference tree provided via -t
(."("A3"8I8
!" !H.."(
J=H/("E
Example: raxmlHPC -f A -t testTree -s testData -m GTRGAMMA -n TEST
((*!.>
4 4
t1 ACGT
t2 AATT
t3 ATAT
t4 CCGT
>
((t1,t2),(t3,t4));
.(8.
""3"."((
..I8"(!"
."5(7!"
"3"
-f b draw bipartition information on a tree provided with -t (typically the best-
known ML tree) based on multiple trees (e.g., from a bootstrap) in a file
specified by -z
Example: raxmlHPC -f b -t ref -z trees -m GTRCAT -n TEST
-f B optimize br-len scaler and other model parameters (GTR, alpha, etc.) on a
tree provided with -t. The input tree passed via -t needs to contain branch
lengths. The branch lengths will not be optimized, just scaled by a single
13
common value.
""(.(."B".
<15>(>AA...!"A(IA7
""(!""(R8
.("(("
.8!"( .!"
!" ,- ." . ( " E (
(6*M.(!"!"
(5"!(Y!*(67
" " " ( 5( *
(6798.!8I."
!"G
Example: raxmlHPC -s alg.phy -t tree -m GTRGAMMA -f B -q part -n TEST
-f c check if the alignment can be properly read by RAxML
Example: raxmlHPC -f c -m GTRCAT -s alg -n TEST
-f C ancestral sequence test for my PhD student Jiajie Zhang, users will also
need to provide a list of taxon names via -Y separated by white-spaces
.(!(*6(
. " ! " 3"
"88!"!
18.!.A>
'I("5*.7!!3"
8!""3" -Y8!" !"
3"."( !I 5(7"
!("3".!I
6"!""
!"8 . (( " " " 3"
"88"""8.."
!!."""3""
!M""I5*6"
7 "( *. 5(7
*.
.L"!"" ..
8!8."!8
((
Example: raxmlHPC -f C -Y candidateTaxonNames -m GTRGAMMA -t tree -s alg
-n TEST
-f d new rapid hill-climbing
DEFAULT: ON
!"!
" "8
14
!!""
((>(>AA("A"A%$%$$XA%%&P*$$X*$$&X*@F(*%
Example: raxmlHPC -f d -m GTRCAT -p 12345 -s alg -n TEST
-f D execute one or more rapid hill-climbing searches that will also generate
RELL bootstraps
( ! "3 " !. ((>
(>AA..."A(A#@%#QX .
( . " . (
+(".H
"A!"((("
Example: raxmlHPC -f D -m GTRCAT -p 12345 -s alg -n TEST
-f e optimize model parameters+branch lengths for given input tree
=(( -t (
Example:raxmlHPC -f e -t ref -m GTRGAMMA -s alg -n TEST
-f E execute very fast experimental tree search, at present only for testing
( . " ! " .
(6 !!."
1(>(>AA"A!A
Example: raxmlHPC -f E -m GTRCAT -p 12345 -s alg -n TEST
-f F execute fast experimental tree search, at present only for testing
( . " ! " .
(6 !!."
1(>(>AA"A!A
Example: raxmlHPC -f F -m GTRCAT -p 12345 -s alg -n TEST
-f g compute per site log Likelihoods for one ore more trees passed via -z and
write them to a file in treepuzzle format that can be read by CONSEL
The model parameters will be estimated on the first tree only!
Example: raxmlHPC -f g -s alg -m GTRGAMMA -z trees -n TEST
-f G compute per site log Likelihoods for one ore more trees passed via -z and
write them to a file in treepuzzle format that can be read by CONSEL.
The model parameters will be re-estimated for each tree!
Example: raxmlHPC -f G -s alg -m GTRGAMMA -z trees -n TEST
-f h compute log likelihood test (SH-test) between best tree passed via -t and a
bunch of other trees passed via -z
The model parameters will be estimated on the first tree only!
15
Example: raxmlHPC -f h -t ref -z trees -s alg -m GTRGAMMA -n TEST
-f H compute log likelihood test (SH-test) between best tree passed via -t and a
bunch of other trees passed via -z
The model parameters will be re-estimated for each tree !
Example: raxmlHPC -f H -t ref -z trees -s alg -m GTRGAMMA -n TEST
-f i calculate IC and TC scores (Salichos and Rokas 2013
(>AA..."AABA@QXAX@@QA!A%%#$) on a reference
tree provided with -t based on multiple trees (e.g., from a bootstrap) in
a file specified by -z
"!.(( .."
>
(>AA!BA"AA$%@A$A$XA$&%" (D
!0BD &P1'9$62.
(>AAA%$%%$%A$$P#!(
Warning: !/A /""""RE
(("."((8(
IbipartitionList.c"
#define BIP_FILTER
Example: raxmlHPC -f i -m GTRCAT -t referenceTree -z bootstrapTrees -n
TEST
-f I a simple tree rooting algorithm for unrooted trees. It roots the tree by
rooting it at the branch that best balances the subtree lengths (sum over
branches in the subtrees) of the left and right subtree. A branch with an
optimal balance does not always exist! You need to specify the tree you want
to root via -t.
Example: raxmlHPC -f I -m GTRCAT -t unrootedTree -n TEST
-f j generate a bunch of bootstrapped alignment files from an original alignment
file. You need to specify a seed with -b and the number of replicates
with -#
Example: raxmlHPC -f j -b 12345 -# 100 -s alg -m GTRCAT -n TEST
Warning: 98!R("!
!."3""(.
("!(I-q"*(
(*(G
-f J Compute SH-like support values on a given tree passed via -t.
( . "( * (( "
16
(>AA..."A(A$PP&#(("
*.!Z(!((*
99 599 "7(8.
((99 !("(
!""!
Example:raxmlHPC -f J -p 12345 -m GTRGAMMA -s alg -t tree -n TEST
-f k Fix long branch lengths in partitioned data sets with missing data using
the branch length stealing algorithm.
This option only works in conjunction with "-t", "-M", and "-q".
It will print out a tree with shorter branch lengths, but having the same
likelihood score.
(I!"(.
1"(""!""!
!(!I" !
" "".
"I"
!(!"" !
("(.!
"""(!.""
"((!""
.8!"
Example: raxmlHPC -f k -m GTRGAMMA -s alg -q part -M -t tree -n TEST
9."I"."..
I">RaxML_stolenBranchLengths.TEST
-f m compare bipartitions between two bunches of trees passed via "-t" and "-z"
respectively. This will return the Pearson correlation between all
bipartitions found in the two tree files. A file called
RAxML_bipartitionFrequencies.outpuFileName will be printed that contains the
pair-wise bipartition frequencies of the two sets
Example: raxmlHPC -f m -t trees1 -z trees2 -s alg -m GTRCAT -n TEST
-f n compute the log likelihood score of all trees contained in a tree file
provided by -z
The model parameters will be estimated on the first tree only!
Example:raxmlHPC -f n -z trees -s alg -m GTRGAMMA -n TEST
-f N compute the log likelihood score of all trees contained in a tree file
provided by -z
The model parameters will be re-estimated for each tree!
Example:raxmlHPC -f N -z trees -s alg -m GTRGAMMA -n TEST
-f o old and slower rapid hill-climbing without the heuristic cutoff described in
(>AA("A"A%$%$$XA%%&P*$$X*$$&X*@F(*%
!(.("".
17
(""!"#
Example: raxmlHPC -f o -p 12345 -m GTRCAT -s alg -n TEST
-f p perform pure stepwise MP addition of new sequences to an incomplete starting
tree and exit
Example:raxmlHPC -f p -t ref -p 12345 -s alg -m GTRCAT -n TEST
-f q fast quartet calculator
(."""!3!(
.""6(.(
"(58*.7 -t
( . I 3
""1"38".(6
!N>57"("I"!
3857"3857"3!(*("I
3"I""@("*!"
(
1(!!3"I8-Y(G
(35(.3"
!"!A7-# -N("!.
3.
Example 1: raxmlHPC -m GTRGAMMA -t tree -s alg -f q -p 12345 -n TEST
(.(3
Example 2: raxmlHPC -m GTRGAMMA -t tree -s alg -f q -p 12345 -N 100 -n TEST
(.%$$"3
(.I">RaxML_quartets.TEST
>
Taxon names and indexes:
Cow 1
Carp 2
Chicken 3
Human 4
Loach 5
Mouse 6
Rat 7
Seal 8
Whale 9
Frog 10
1 2 | 3 4: -2640.417355
18
1 3 | 2 4: -2640.810748
1 4 | 2 3: -2638.359608
1 2 | 3 5: -2552.181311
1 3 | 2 5: -2543.674965
...
18 " 8 3 (
(8 ! "8 1 2 | 3 4: -2640.417355 3 ((Cow,Carp),
(Chicken, Human)) ! -2640.417355 .
< ! ("I" ( " "( . "(
I.3"(".<
-f r compute pairwise Robinson-Foulds (RF) distances between all pairs of trees
in a tree file passed via -z. If the trees have node labels represented as
integer support values the program will also compute two flavors of the
weighted Robinson-Foulds (WRF) distance
Example: raxmlHPC -m GTRCAT -z trees -f r -n TEST
.N!)1""(>
%B((!("8
((!("8
M"((!"(
(!.5".1"7>
0 1: 8 0.125000
. 0 1 ". 0 1 I5
I " 78. 8 ( 1" 0.12500
61""(%PS
6A1"""(1./0128.
!
!61".$$%$(
("!(5(73!.
(8%PS!(3$%
-f R compute all pairwise Robinson-Foulds (RF) distances between a large
reference tree passed via -t and many smaller trees (that must have a
subset of the taxa of the large tree) passed via -z.
This option is intended for checking the plausibility of very large
phylogenies that can not be inspected visually any more.
Example: raxmlHPC -f R -m GTRCAT -t hugeTree -z manySmallTrees
-f s split up a multi-gene partitioned alignment into the respective
subalignments
Example:raxmlHPC -f s -q part -s alg -m GTRCAT -n TEST
Warning: 9*.
( !(I".("
19
part1part28"..I"
part1.phypart2.phy
-f S compute site-specific placement bias using a leave one out test inspired by
the evolutionary placement algorithm
**(("!*("I"""A"".
("8
(>AA!BA"A&$A#AQ%
+ !" 5("*. 7**
""(8"*("I""(!
8 3*(
1 " . .. ! 6 5 ! "345667 !
"""(("
.("
(!"..
2" . (" ! " ..
(!8."(",-,-!"
",-,-"5!!7.
("("! .."(
("!
18.""7,-"!""(!,-,-
"(!"
8.! 7,- "8.
!
Example: raxmlHPC -f S -s alg -t tree -m GTRGAMMA -n TEST
(!("
!MA(!"."(!58
%&7(!3"9'
(.(I">
RaxML_SiteSpecificPlacementBias.TEST ." " (
(8!.(>
20
(".($$&$$.
".""28
("".8
("
-f t do randomized tree searches on one fixed starting tree
"."("I5-N-#7!6"
M""88.((
<5(*!76I
Example:raxmlHPC -f t -t -m GTRCAT -s alg -p 12345 -n TEST
-f T do final thorough optimization of ML tree from rapid bootstrap search in
stand-alone mode
( . " 68 8
<8*(""
!"-f a
Example: raxmlHPC -p 12345 -m GTRGAMMA -s alg -f T -t tree -n TEST
-f u execute morphological weight calibration using maximum likelihood, this will
return a weight vector. you need to provide a morphological alignment and a
reference tree via -t
( . ." ! ("
"."!"(..
IN"!"""3-a
(""!("!!
("5-f v(718"(((>
E("(>AA!BA"A&$A#AQ%
1" (>AA(A(AB(C(D0DPP&Q#Q0D(
S# SS1(S1(S1KB(S#1S#-PP&Q#Q
Example: raxmlHPC -f u -m BINGAMMA -t molecularTree -s
morphologicalAlignment
-f v classify a bunch of environmental sequences into a reference tree using
thorough read insertions you will need to start RAxML with a non-
comprehensive reference tree and an alignment containing all sequences
(reference + query)
1 (!" ! 8 >
21
(>AA!BA"A&$A#AQ%
.(""(!""(I!("8
(I"""IIE"!pplacer
5 (>AA!""A(("A7 ( E< 5E
<"7!
"I!"((>
(>AA...(A"A! S#S1%$%#X%S1B($$#%$$Q
Example: raxmlHPC -f v -s alg -t referenceTree -m GTRCAT -n TEST
!!3.M3"!"8
"L"8"("
!""!!"".( !
.("!.
'I"(!!"
Example 1: raxmlHPC -f e -m GTRGAMMA -s referenceAlignment -t referenceTree
-n PARAMS
.I">RAxML_binaryModelParameters.PARAMS .""
E<*(6(>
Example 2: raxmlHPC -f v -R RAxML_binaryModelParameters.PARAMS
-t RAxML_result.PARAMS -s alg -m GTRGAMMA -n TEST2
Warning: 98.I> !
(%058GTRGAMMA GTRCAT7G"8
.GTRCAT("(-HN
G8!"-t(
"""("I-m"
!!"*(6"(
.".
GTRGAMMA.GTRCAT!
((.I-R(
-f V classify a bunch of environmental sequences into a reference tree using
thorough read insertions you will need to start RAxML with a non-
comprehensive reference tree and an alignment containing all sequences
(reference + query)
(!E<!(" *
"("("! !
!.((>(>AA..."AABA%$A%A!A&Q#
Example: raxmlHPC -f V -q part -s alg -t referenceTree -m GTRCAT -n TEST
Warning: (!L"!*0
.* G
22
-f w compute ELW test on a bunch of trees passed via -z
The model parameters will be estimated on the first tree only!
/( E ) 8
(>AA..."A(A%%XQ@8!
Example:raxmlHPC -f w -m GTRGAMMA -s alg -z trees -n TEST
-f W compute ELW test on a bunch of trees passed via -z
The model parameters will be re-estimated for each tree
Example: raxmlHPC -f W -m GTRGAMMA -s alg -z trees -n TEST
-f x compute pair-wise ML distances, ML model parameters will be estimated on an
MP starting tree or a user-defined tree passed via -t, only allowed for
GAMMA-based models of rate heterogeneity
( . B "( (*. " 5" 7 .
3" !
(5'8((("7.
("I58*.76(.
(!(( (6(
"((*."
Example: raxmlHPC -f x -p 12345 -s alg -m GTRGAMMA -n TEST
-f y classify a bunch of environmental sequences into a reference tree using
parsimony you will need to start RAxML with a non-comprehensive reference
tree and an alignment containing all sequences (reference + query)
" -f v ".M"
(!("!"R"(
!!*("="!("
!!"
Example: raxmlHPC -f y -m GTRCAT -s alg -t referenceTree -n TEST
Warning: (8("
83((A"!!"R
"!3((""".
6G
-F enable ML tree searches under CAT model for very large trees without
switching to GAMMA in the end (saves memory).
This option can also be used with the GAMMA models in order to avoid the
thorough optimization of the best-scoring ML tree in the end.
DEFAULT: OFF
) "" / ! 8
(."'*"
(6!'!" !.
"!A"5'!
/7"(
23
Example: raxmlHPC -F -m GTRCAT -p 12345 -s alg -N 10 -n TEST
-g specify the file name of a multifurcating constraint tree this tree does not
need to be comprehensive, i.e. must not contain all taxa
( !3 " "! ! . > 57 !
"("(88"
8""!88.!
(!G57!"(
" 6 8
( ." (!" 5
.G7!"(."
<*"".""!((G
18*!"(.
"
Example: raxmlHPC -g constraintTree -m GTRGAMMA -p 12345 -s alg -n TEST
-G enable the ML-based evolutionary placement algorithm heuristics by
specifying a threshold value (fraction of insertion branches to be evaluated
using thorough insertions under ML).
( " "B" . *! *! , ( ( (
("!!$%5%$S!""!
7 """A( *M 1
" " ((>
(>AA!BA"A&$A#AQ%
Example: raxmlHPC -f v -G 0.1 -s alg -t referenceTree -m GTRCAT -n TEST
-h Display this help message.
Example: raxmlHPC -h
-H Disable pattern compression.
DEFAULT: ON
( . "( ( !
""""("
((""((!
Example: raxmlHPC -H -s alg -p 12345 -m GTRCAT -n TEST
Warning: ("..
-i Initial rearrangement setting for the subsequent application of topological
changes phase
(.("!5!.!(
(7(."( .*"!<5
(*!7"R!.
24
"(.("I!%$88.
".%%$.!(
(
Example: raxmlHPC -i 10 -s alg -m GTRCAT -p 12345 -n TEST
-I a posteriori bootstopping analysis. Use:
-I autoFC for the frequency-based criterion
-I autoMR for the majority-rule consensus tree criterion
-I autoMRE for the extended majority-rule consensus tree criterion
-I autoMRE_IGN for metrics similar to MRE, but include bipartitions under
the threshold whether they are compatible or not. This emulates MRE but
is faster to compute.
You also need to pass a tree file containing several bootstrap replicates
via -z
( . " ( "" 8 8
!"(L"R("!((8
(8 ! "(8 ! "8 %$$ (
("(("!.*""
("(.P$("""!L"
HP$!%$$.L"8"
!N!"""> autoMRE !
!!5%$$$7autoMRE_IGNR!
( "( ((>
(>AA("A"(A%$%$$XAQX*#*&@*$$$*XK%#F(*%
Example: raxmlHPC -m GTRCAT -z RAxML_bootstrap.BS -I autoMRE -n TEST
9 8 ! I " ( "
""cat"
Example:cat RAxML_bootstrap.BS_1 RAxML_bootstrap.BS_2 > allBootstraps
-j Specifies that intermediate tree files shall be written to file during the
standard ML and BS tree searches.
DEFAULT: OFF
.(("(!"
I . I ">
RAxML_checkpoint.TEST.0, RAxML_checkpoint.TEST.1, "
Example: raxmlHPC -j -m GTRGAMMA -s alg -p 12345 -n TEST
-J Compute majority rule consensus tree with "-J MR" or extended majority rule
consensus tree with "-J MRE" or strict consensus tree with "-J STRICT". For
a custom consensus threshold >= 50%, specify T_<NUM>, where 100 >= NUM >=
50.
Options "-J STRICT_DROP" and "-J MR_DROP" will execute an algorithm that
identifies dropsets which contain rogue taxa as proposed by Pattengale et
al. in the paper "Uncovering hidden phylogenetic consensus".
You will also need to provide a tree file containing several UNROOTED trees
via "-z"
25
(".M!8!"
! I 8
(688!<.!G
="!.((.(G
1">
(>AA...""""A""A"A(A%XXXP$#%$$$$$&
1!>
(>AA(A(AB((D0DPX%$X@0D(S#S1
S1(S1(S1KB(S#1S#-PX%$X@
.(."(B"XPS
B"
Example: raxmlHPC -J MRE -z trees -m GTRCAT -n TEST
Example: raxmlHPC -J T_75 -z trees -m GTRCAT -n TEST
(.I!(
B18(((
Example: raxmlHPC -J MR_DROP -z trees -m GTRCAT -n TEST
-k Specifies that bootstrapped trees should be printed with branch lengths.
The bootstraps will run a bit longer, because model parameters will be
optimized at the end of each replicate under GAMMA or GAMMA+P-Invar
respectively.
DEFAULT: OFF
Example: raxmlHPC -b 12345 -p 12345 -# 100 -k -s alg -m GTRGAMMA -n TEST
-K Specify one of the multi-state substitution models (max 32 states)
implemented in RAxML.
Available models are: ORDERED, MK, GTR
DEFAULT: GTR model
E8!(M""*
"" !("!*""
("I *Z . (( 8 (
M"*(G
Example: raxmlHPC -p 12345 -m MULTIGAMMA -s multiStateAlignment -n TEST
-L Compute consensus trees labeled by IC supports and the overall TC value as
proposed in Salichos and Rokas 2013.
Compute a majority rule consensus tree with -L MR or an extended majority
rule consensus tree with -L MRE.
For a custom consensus threshold >= 50%, specify -L T_<NUM>, where 100 >=
NUM >= 50.
26
You will of course also need to provide a tree file containing several
UNROOTED trees via -z!
(."(/ /""8"
"((>
(>AA..."AABA@QXAX@@QA!A%%#$
"!.(( .."
>
(>AA!BA"AA$%@A$A$XA$&%" (D
!0BD &P1'9$62.
Warning: !/A /""""RE
(("."((8(
IbipartitionList.c"
#define BIP_FILTER
""!.."
Example: raxmlHPC -m GTRCAT -L MRE -z trees -n TEST
-m Model of Binary (Morphological), Nucleotide, Multi-State, or Amino Acid
Substitution:
("("!"(""
("!!(.!8"
( ( ( ("I" !
"("I(I8!-q
(!."!( -m
."!98
.(((8""(
6CAT6GAMMA
8CAT.".CAT
!CATI"!"CAT8.
IGAMMA(((!
!!(GAMMA
R (( X " .
!!3"
R((ASC_".(("
""""!!A("
" 5 " (" !
" 8 " "" ! 8 8 8
(>AA!BA"AP$A&AQ%#7
1-9(!.6!9<
H""98!"""
(("""(""
"8..
.I !>
AAAA----MR
27
" " - "5
*"7"(""-8M.R
" A .8 . . "" .
"""!""
)9<3!
"")""8!"8-m
ASC_GTRCAT".-V(."!"
('.""!
8. M(*!5/7
."""8 "/"
.-V57"('!
."""5-m ASC_GTRGAMMA"7
18 8 ! %X ! . ("! ( !
" "" . 8. .M"""
(18(!**asc-corr(
BINARY:
-m BINCAT[X] Optimization of site-specific evolutionary rates which are
categorized into numberOfCategories distinct rate
categories for greater computational efficiency. Final tree
might be evaluated automatically under BINGAMMA, depending
on the tree search option.
With the optional "X" appendix you can specify a ML
estimate of base frequencies.
-m BINCATI[X] Optimization of site-specific evolutionary rates which are
categorized into numberOfCategories distinct rate
categories for greater computational efficiency. Final tree
might be evaluated automatically under BINGAMMAI, depending
on the tree search option.
With the optional "X" appendix you can specify a ML
estimate of base frequencies.
-m ASC_BINCAT[X] Optimization of site-specific evolutionary rates which are
categorized into numberOfCategories distinct rate
categories for greater computational efficiency. Final tree
might be evaluated automatically under BINGAMMA, depending
on the tree search option.
With the optional "X" appendix you can specify a ML
estimate of base frequencies.
The ASC prefix will correct the likelihood for
ascertainment bias. You will also need to specify the
correction type via --asc-corr!
-m BINGAMMA[X] GAMMA model of rate heterogeneity (alpha parameter will be
estimated). With the optional "X" appendix you can specify
a ML estimate of base frequencies.
-m ASC_BINGAMMA[X] GAMMA model of rate heterogeneity (alpha parameter will be
estimated). The ASC prefix will correct the likelihood for
28
ascertainment bias.
With the optional "X" appendix you can specify a ML
estimate of base frequencies. You will also need to specify
the correction type via --asc-corr!
-m BINGAMMAI[X] Same as BINGAMMA, but with estimate of proportion of
invariable sites. With the optional "X" appendix you can
specify a ML estimate of base frequencies.
NUCLEOTIDES:
-m GTRCAT[X] GTR + Optimization of substitution rates + Optimization of
site-specific evolutionary rates which are categorized into
numberOfCategories distinct rate categories for greater
computational efficiency. Final tree might be evaluated
under GTRGAMMA, depending on the tree search option.
With the optional "X" appendix you can specify a ML
estimate of base frequencies.
-m GTRCATI[X] GTR + Optimization of substitution rates + Optimization of
site-specific evolutionary rates which are categorized into
numberOfCategories distinct rate categories for greater
computational efficiency. Final tree might be evaluated
under GTRGAMMAI, depending on the tree search option.
With the optional "X" appendix you can specify a ML
estimate of base frequencies.
-m ASC_GTRCAT[X] GTR + Optimization of substitution rates + Optimization of
site-specific evolutionary rates which are categorized into
numberOfCategories distinct rate categories for greater
computational efficiency. Final tree might be evaluated
under GTRGAMMA, depending on the tree search option.
With the optional "X" appendix you can specify a ML
estimate of base frequencies.
The ASC prefix will correct the likelihood for
ascertainment bias. You will also need to specify the
correction type via --asc-corr!
-m GTRGAMMA[X] GTR + Optimization of substitution rates + GAMMA model of
rate heterogeneity (alpha parameter will be estimated).
With the optional "X" appendix you can specify a ML
estimate of base frequencies.
-m ASC_GTRGAMMA[X] GTR + Optimization of substitution rates + GAMMA model of
rate heterogeneity (alpha parameter will be estimated).
The ASC prefix will correct the likelihood for
ascertainment bias.
With the optional "X" appendix you can specify a ML
estimate of base frequencies. You will also need to specify
the correction type via --asc-corr!
-m GTRGAMMAI[X] Same as GTRGAMMA, but with estimate of proportion of
invariable sites. With the optional "X" appendix you can
specify a ML estimate of base frequencies.
MULTI-STATE:
29
-m MULTICAT[X] Optimization of site-specific evolutionary rates which are
categorized into numberOfCategories distinct rate
categories for greater computational efficiency. Final tree
might be evaluated automatically under MULTIGAMMA,
depending on the tree search option.
With the optional "X" appendix you can specify a ML
estimate of base frequencies.
-m MULTICATI[X] Optimization of site-specific evolutionary rates which are
categorized into numberOfCategories distinct rate
categories for greater computational efficiency. Final tree
might be evaluated automatically under MULTIGAMMAI,
depending on the tree search option.
With the optional "X" appendix you can specify a ML
estimate of base frequencies.
-m ASC_MULTICAT[X] Optimization of site-specific evolutionary rates which are
categorized into numberOfCategories distinct rate
categories for greater computational efficiency. Final tree
might be evaluated automatically under MULTIGAMMA,
depending on the tree search option.
With the optional "X" appendix you can specify a ML
estimate of base frequencies. The ASC prefix will correct
the likelihood for ascertainment bias. You will also need
to specify the correction type via --asc-corr!
-m MULTIGAMMA[X] GAMMA model of rate heterogeneity (alpha parameter will be
estimated). With the optional "X" appendix you can specify
a ML estimate of base frequencies.
-m ASC_MULTIGAMMA[X] GAMMA model of rate heterogeneity (alpha parameter will be
estimated). The ASC prefix willl correct the likelihood for
ascertainment bias. With the optional "X" appendix you can
specify a ML estimate of base frequencies. You will also
need to specify the correction type via --asc-corr!
-m MULTIGAMMAI[X] Same as MULTIGAMMA, but with estimate of proportion of
invariable sites. With the optional "X" appendix you can
specify a ML estimate of base frequencies.
You can use up to 32 distinct character states to encode
multi-state regions, they must be used in the following
order:
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J,
K, L, M, N, O, P, Q, R, S, T, U, V
i.e., if you have 6 distinct character states you would use
0, 1, 2, 3, 4, 5 to encode these.
The substitution model for the multi-state regions can be
selected via the "-K" option
AMINO ACIDS:
-m PROTCATmatrixName[F|X] specified AA matrix + Optimization of substitution rates +
Optimization of site-specific evolutionary rates which are
categorized into numberOfCategories distinct rate
categories for greater computational efficiency. Final tree
30
might be evaluated automatically under
PROTGAMMAmatrixName[F|X], depending on the tree search
option.
With the optional "X" appendix you can specify a ML
estimate of base frequencies.
-m PROTCATImatrixName[F|X] specified AA matrix + Optimization of substitution rates +
Optimization of site-specific evolutionary rates which are
categorized into numberOfCategories distinct rate
categories for greater computational efficiency.
Final tree might be evaluated automatically under
PROTGAMMAImatrixName[F|X], depending on the tree search
option. With the optional "X" appendix you can specify a ML
estimate of base frequencies.
-m ASC_PROTCATmatrixName[F|X] specified AA matrix + Optimization of substitution rates +
Optimization of site-specific evolutionary rates which are
categorized into numberOfCategories distinct rate
categories for greater computational efficiency.
Final tree might be evaluated automatically under
PROTGAMMAmatrixName[F|X], depending on the tree search
option.
With the optional "X" appendix you can specify a ML
estimate of base frequencies. The ASC prefix will correct
the likelihood for ascertainment bias. You will also need
to specify the correction type via --asc-corr!
-m PROTGAMMAmatrixName[F|X] specified AA matrix + Optimization of substitution rates +
GAMMA model of rate heterogeneity (alpha parameter will be
estimated).
With the optional "X" appendix you can specify a ML
estimate of base frequencies.
-m ASC_PROTGAMMAmatrixName[F|X] specified AA matrix + Optimization of substitution
rates + GAMMA model of rate heterogeneity (alpha parameter
will be estimated). The ASC prefix will correct the
likelihood for ascertainment bias.
With the optional "X" appendix you can specify a ML
estimate of base frequencies. You will also need to specify
the correction type via --asc-corr!
-m PROTGAMMAImatrixName[F|X] Same as PROTGAMMAmatrixName[F|X], but with estimate of
proportion of invariable sites.
With the optional "X" appendix you can specify a ML
estimate of base frequencies.
Available AA substitution models:
DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, LG,
MTART, MTZOA, PMB, HIVB, HIVW, JTTDCMUT, FLU, STMTREV, DUMMY, DUMMY2, AUTO,
LG4M, LG4X, PROT_FILE, GTR_UNLINKED, GTR
With the optional "F" appendix you can specify if you want to use empirical
base frequencies. AUTOF and AUTOX are not supported any more, if you
specify AUTO it will test prot subst. models with and without empirical
base frequencies now!
31
Please note that for partitioned models you can in addition specify the per-
gene AA model in the partition file. Also note that if you estimate AA GTR
parameters on a partitioned dataset, they will be linked (estimated jointly)
across all partitions to avoid over-parametrization
Warning: )LG4X(8((8
"!(8I(
8!"('@
&!(5#!.#!79
#.#(".
%$5@(#7
!("!"..("
%$5(Q@("((>
(>AA!BA"AQA%$AQ%!(!7
88'@".("!3"8
.!5'@18'@17.!
!3"5'@8'@7
+('@8!3"
5shared/linked7!@"!'@
%Q(
)I!!'@(
(".((
(. /0R /"8(
(!""8"((!
((."!@8".!
!3"
9:&+&
3%:;<)=%:;)=%:;<<=%:;<>"&?
( . . " ( " / (( !
-9I'
Example: raxmlHPC -m GTRCAT -s alg -p 12345 -n TEST
( . . " ( " / (( !
-98I'U<*
Example: raxmlHPC -m GTRCATI -s alg -p 12345 -n TEST
( . . " ( " / (( !
-9 !
!3"8!("!3"
Example: raxmlHPC -m GTRCATX -s alg -p 12345 -n TEST
( . . " ( " ' !
-9
Example: raxmlHPC -m GTRGAMMA -s alg -p 12345 -n TEST
( . . " ( " ' !
""!"-9
Example: raxmlHPC -m ASC_GTRGAMMA -s alg -p 12345 -n TEST
32
( . . " ( " ( ' 5
7""!"-9
Example: raxmlHPC -m ASC_GTRCAT -V -s alg -p 12345 -n TEST
( . . " ( " ' !
Example: raxmlHPC -m BINGAMMA -s alg -p 12345 -n TEST
( . . " ( " ' !
(!3"
".)'
Example: raxmlHPC -m PROTGAMMAWAG -s alg -p 12345 -n TEST
( . . " ( " ' !
( (" !3" '
Example: raxmlHPC -m PROTGAMMALGF -s alg -p 12345 -n TEST
(.."("'U<* !
( !
!3"'
Example: raxmlHPC -m PROTGAMMAILGX -s alg -p 12345 -n TEST
( . . " ( " ' !
(("!3"'
!"
Warning: .*(6".
!%Q('
Example: raxmlHPC -m PROTGTRGAMMA -s alg -p 12345 -n TEST
(.."."5.
"(7( !
!3"". ."
!.>DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62,
MTMAM, LG, MTART, MTZOA, PMB, HIVB, HIVW, JTTDCMUT, FLU, DUMMY, DUMMY2
."> LG4M, LG4X, PROT_FILE,GTR_UNLINKED, GTR!
.."..("!3"
"!"""."
–auto-prot=ml|bic|aic|aicc(
Example: raxmlHPC -m PROTGAMMAAUTO -s alg -p 12345 -n TEST
-M Switch on estimation of individual per-partition branch lengths. Only
has effect when used in combination with "-q"
Branch lengths for individual partitions will be printed to separate
files
33
A weighted average of the branch lengths is computed by using the
respective partition lengths
DEFAULT: OFF
.((*(!"9
""!!(
.01".! !(8!
.01 ( . /.012 (. ! (
..!(
( ! ( 8 . ( I ! "
(."(*("!
Example: raxmlHPC -p 12345 -M -m GTRGAMMA -s alg -q part -n TEST
-n Specifies the name of the output file.
(.("I(-n.((
(I".."I."
"
!..I".
("I*(..(*.(I
!(
Example: raxmlHPC -p 12345 -m GTRGAMMA -s alg
-n MySuperDuperRAxMLOutputFileName
-o Specify the name of a single outgroup or a comma-separated list of
outgroups, e.g., -o Rat or -o Rat,Mouse, in case that multiple outgroups are
not monophyletic the first name in the list will be selected as outgroup,
don't leave spaces between taxon names!
! ( "" ! ( ! ((
("(AI57.(! !(("
.I(("
..(
Z((B.(88
Example: raxmlHPC -s alg -p 12345 -m GTRGAMMA -o Rat,Mouse -n TEST
A comment on using outgroups: How I would do it.
H((
H("!.(!.
1. R5UR"7(
8E<5>(>AA!BA"A&$A#AQ%7("
(57(
>
%="AM(
=H*!(.(
!(((
34
#=(M""!("!.
("
@=("(5.7!"(88.
(!"!(
5(!("("I""7!5""
7
-O Disable check for completely undetermined sequence in alignment.
The program will not exit with an error message when "-O" is specified.
DEFAULT: check enabled
6.3"
"!"(""58-,N,?,X"7"H
!3".("
9...""3"
("8...
.(
Example: raxmlHPC -s alg -p 12345 -m GTRGAMMA -O -n TEST
-p Specify a random number seed for the parsimony inferences. This allows you
to reproduce your results and will help me debug the program.
1(A3!68(
("I(M
%#@P ()("!*(.3
8(..("
(.5("!7
3!6(.("(
("(6
Example: raxmlHPC -s alg -p 2352890 -m GTRGAMMA -n TEST
-P Specify the file name of a user-defined AA (Protein) substitution model.
This file must contain 420 entries, the first 400 being the AA substitution
rates (this must be a symmetric matrix) and the last 20 are the empirical
base frequencies
98("!-m PROTGAMMAWAG (.
.."!(
.'!!
.WAG
! . . ( ! ( 8
I!"("I
(I
Example: raxmlHPC -s alg -p 12345 -P myProteinModel -m PROTGAMMAWAG
-n TEST
-q Specify the file name which contains the assignment of models to alignment
partitions for multiple models of substitution. For the syntax of this file
please consult the manual.
35
(.("!!!."
!"""M(
!
.("!!!5!W(7*
!88*''8(*((8'8
("!3".(6!"(
"""!M(58-9
8("7("!(!!"((
I8!(
1-9BDNA"(I8!
("!("58WAGLG7
.!(1H("!BIN!*
MULTI
9.8!.6("I"("""
((ASC_(88ASC_WAGASC_DNA
!!("I"(.!
!3"8H((X(88DNAXLGX
!.("!3"5!!(*I
(.7H.88WAGFJTTF
!.(!.!("I"(8
!("I!-P ( !("!(
.WAG!"8.("!(I
3"88[myProtenSubstitutionModelFileName]
!.(!""-9("
("!-m GTRGAMMA88-m PROTGAMMAWAG..
"!(*!.
!(-9.%8$$$(!.%5(%WP$$7
5(P$%W%8$$$7!(I
!.>
DNA, gene1 = 1-500
DNA, gene2 = 501-1000
!.!!3"!I(.>
DNAX, gene1 = 1-500
DNA, gene2 = 501-1000
6I(.""".>
ASC_DNA, gene1 = 1-500
DNA, gene2 = 501-1000
!%"8(%W$$8$$W%8$$$
("!.>
DNA, gene1 = 1-200, 800-1,000
DNA, gene2 = 201-799
="""(8!."
!""(%"("!>
DNA, gene1codon1 = 1-500\3
36
DNA, gene1codon2 = 2-500\3
DNA, gene1codon3 = 3-500\3
DNA, gene2 = 501-1000
!"!#"(".>
DNA, gene1codon1andcodon2 = 1-500\3, 2-500\3
DNA, gene1codon3 = 3-500\3
DNA, gene2 = 501-1000
8!("!"!"
(>
JTT, gene1 = 1-500
WAGF, gene2 = 501-800
WAG, gene3 = 801-1000
I"(
"!A(8B-9="
M!M(88./8
'8' "!(8("I.-m
!.(!.8!(8H.>
[prot~myProtenSubstitutionModelFileName], gene1 = 1-500
WAGF, gene2 = 501-800
WAG, gene3 = 801-1000
!!3"!(H.>
JTTX, gene1 = 1-500
WAGX, gene2 = 501-800
WAGX, gene3 = 801-1000
18!""-98.-9(%W
P$$P$%*%8$$$.)'(I!.>
DNA, gene1 = 1-500
WAG, gene2 = 501-1000
(I!.>
BIN, gene1 = 1-500
BIN, gene2 = 501-1000
!*
MULTI, gene1 = 1-500
MULTI, gene2 = 501-1000
Example: raxmlHPC -s alg -m GTRGAMMA -q part -p 12345 -n TEST
-r Specify the file name of a binary constraint tree.
37
This tree does not need to be comprehensive, i.e. must not contain all taxa
(.( A!" "A"9E) /Z
!
98(!"(
.("2"
"(..(6
(""!"
8(.""!"((
).B""
(!
Example: raxmlHPC -s alg -m GTRGAMMA -r constr -p 12345 -n TEST
-R Specify the file name of a binary model parameter file that has previously
been generated with RAxML using the -f e tree evaluation option. The file
name should be: RAxML_binaryModelParameters.runID
("!(8*
(!I8"
( ( I . " -f e
!"
!. -f v (..("M
!".3!" -f q8("(
!G
Example: raxmlHPC -f v -R RAxML_binaryModelParameters.PARAMS
-t RAxML_result.PARAMS -s alg -m GTRCAT -n TEST2
-s Specify the name of the alignment data file in PHYLIP or FASTA format
("!!I.""<= <!
;.!3"I3
).
.(".3"
S3""!.%(P&"" !
"(" #define nmlngth 256 I axml.h
(((8.("!588
"7!<= <I
".(1 ! !""H ( ((
!.(I1!!
(1I
(!((I!M("!(**
(*>(>AA"*AA.A!.AAK
Example: raxmlHPC -s alignment.fasta -m GTRGAMMA -p 12345 -n TEST
-S Specify the name of a secondary structure file. The file can contain "." for
alignment columns that do not form part of a stem and characters "()<>[]{}"
to define stem regions and pseudoknots
38
("! " " ! 9 . M
(*(".(9
I ( -S ." 9
(A
)".(I88-9
&$8""I"!&$
"">
..................((.......))............(.........)........
H.H " B 9 . " "
E8!(""" 8
( ("! ( . > <>[]{} ! ">
..................((.......)).......{....(....}....)........
! &*8 X* %&* ! ""
""("I-A
> S6A, S6B, S6C, S6D, S6E, S7A, S7B, S7C, S7D, S7E, S7F,
S16, S16A, S16B!'%&*5-A S167
" <E 8 ( " (
http://intranet.cs.man.ac.uk/ai//Software/phase/phase-2.0-manual.pdf!"
"(!
Example: raxmlHPC -m GTRGAMMA -p 12345 -S secondaryStructure.txt
-s rna.phy -n TEST
"3."""(
((.8"(988.
( ! -9 ! ) .
( ! " " ""
"""((!M(!
-t Specify a user starting tree file name in Newick format
("II."9."!"
!.!(*
98 " ("! *"( 5 "
7!!.A3"
."
8.("(.
(6
Example: raxmlHPC -s alg -m GTRGAMMA -t tree -p 12345 -n TEST
-T PTHREADS VERSION ONLY! Specify the number of threads you want to run.
Make sure to set "-T" to at most the number of CPUs you have on your
machine, otherwise, there will be a huge performance decrease!
T$!8<.("!-T
Example: raxmlHPC-PTHREADS -T 4 -s alg -m GTRGAMMA -p 12345 -n TEST
-u use the median for the discrete approximation of the GAMMA model of rate
39
heterogeneity
DEFAULT: OFF
!("!(8.!!"
'!("8.
"
Example: raxmlHPC -p 12345 -u -s alg -m GTRGAMMA -n TEST
-U Try to save memory by using SEV-based implementation for gap columns on
large gappy alignments. The technique is described here:
http://www.biomedcentral.com/1471-2105/12/470
This will only work for DNA and/or PROTEIN data and only with the SSE3 or
AVX-vextorized version of the code.
("((((*
.8("".("((
( 5 ! " ! " A(7
!((((!
Example: raxmlHPC -p 12345 -U -s alg -m GTRGAMMA -n TEST
-v Display version information
-(
Example: raxmlHPC -v
-V Disable rate heterogeneity among sites model and use one without rate
heterogeneity instead. Only works if you specify the CAT model of rate
heterogeneity.
DEFAULT: use rate heterogeneity
("!I.
8"
Example: raxmlHPC -m GTRCAT -s alg -p 12345 -V -n TEST
-w FULL (!) path to the directory into which RAxML shall write its output files
DEFAULT: current directory
9!."..(I9
("!!((G
Example: raxmlHPC -m GTRCAT -p 12345 -s alg
-w /home/stamatak/Desktop/myAnalysys -n TEST
-W Sliding window size for leave-one-out site-specific placement bias algorithm
only effective when used in combination with -f S
40
DEFAULT: 100 sites
-I..6!*!(8%$$
(
Example: raxmlHPC -f S -s alg -t tree -m GTRGAMMA -N 100 -W 200 -n TEST
-x Specify an integer number (random seed) and turn on rapid bootstrapping
CAUTION: unlike in previous versions of RAxML will conduct rapid BS
replicates under the model of rate heterogeneity you specified via -m and
not by default under CAT
.((("
(>AA!BA"APXAPAXP
Example: raxmlHPC -x 12345 -p 12345 -# 100 -m GTRCAT -s alg -n TEST
="".(((5("""78
>
Example: raxmlHPC -x 12345 -p 12345 -# AUTO_MRE -m GTRCAT -s alg -n TEST
"!*"!("
-f a (>
Example: raxmlHPC -x 12345 -p 12345 -# AUTO_MRE -m GTRCAT -s alg -f a
-n TEST
-X Same as the "-y" option below, however the parsimony search is more
superficial.
RAxML will only do a randomized stepwise addition order parsimony tree
reconstruction without performing any additional SPRs.
This may be helpful for very broad whole-genome datasets, since this can
generate topologically more different starting trees.
DEFAULT: OFF
Example: raxmlHPC -X -m GTRCAT -s alg -p 12345 -n TEST
-y If you want to only compute a parsimony starting tree with RAxML specify -y,
the program will exit after computation of the starting tree
DEFAULT: OFF
!."(6(.
"!("! -y(.!"(!
Example: raxmlHPC -y -m GTRCAT -s alg -p 12345 -n TEST
-Y Pass a quartet grouping file name defining four groups from which to draw
quartets
The file input format must contain 4 groups in the following form:
(Chicken, Human, Loach), (Cow, Carp), (Mouse, Rat, Seal), (Whale, Frog);
Only works in combination with -f q !
41
(.8..%$$3!(I3(
Example: raxmlHPC -f q -m GTRGAMMA -t tree -Y quartetFile -n 100 -n TEST
-z Specify the file name of a file containing multiple trees e.g. from a
bootstrap that shall be used to draw bipartition values onto a tree provided
with -t.
It can also be used, for instance to compute per site log likelihoods in
combination with -f g and to read a bunch of trees for a couple of other
options (-f h, -f m, -f n).
(3".!(8"
"!R.(.(
.R((*.
Example: raxmlHPC -f b -m GTRCAT -t mlTree -z bootstrapTrees -n TEST
-#|-N Specify the number of alternative runs on distinct starting trees
In combination with the "-b" option, this will invoke a multiple bootstrap
analysis
Note that "-N" has been added as an alternative since -# sometimes caused
problems with certain MPI job submission systems, since -# is often used
to start comments.
If you want to use the bootstopping criteria specify -# autoMR or -#
autoMRE or -# autoMRE_IGN for the majority-rule tree based criteria (see -I
option) or -# autoFC for the frequency-based criterion.
Bootstopping will only work in combination with -x or -b
DEFAULT: 1 single analysis
("I!"88!-# 10-N 10
("I8."(%$"!%$"6
(
".-b(8.((
".-x.(R".-f a -x
(R"!"
)"-N-# "("""#
"(.""B
".-f j .2!((I
98(("35-f q
(7*("I"("5-f S(73(
("I. !!("!(8.
(..$("$6(.
(
Example: raxmlHPC -p 12345 -s alg -n TEST -m GTRGAMMA -# 20
--mesquite Print output files that can be parsed by Mesquite.
DEFAULT: Off
42
Example: raxmlHPC -p 12345 -s alg --mesquite -n TEST -m GTRGAMMA
--silent Disables printout of warnings related to identical sequences and
entirely undetermined sites in the alignment . The program might run
faster when this is enabled.
DEFAULT: Off
Example: raxmlHPC -p 12345 --silent -s alg -n TEST -m GTRGAMMA
--no-seq-check Disables checking the input MSA for identical sequences and
entirely undetermined sites. Enabling this option may save time,
in particular for large phylogenomic alignments.
Before using this, make sure to check the alignment using the
-f c option!
DEFAULT: Off
Example: raxmlHPC -p 12345 -s alg --no-seq-check -n TEST -m GTRGAMMA
--no-bfgs Disables automatic usage of BFGS method to optimize GTR rates on
unpartitioned DNA datasets . Using BFGS can improve speeds for model
optimization by up to 30%. It's enabled by default when analyzing
single-partition DNA datasets.
DEFAULT: BFGS on
Example: raxmlHPC -p 12345 -s alg --no-bfgs -n TEST -m GTRGAMMA
--asc-corr Allows to specify the type of ascertainment bias correction you wish to
use. There are three types available:
--asc-corr=lewis: the standard correction by Paul Lewis
--asc-corr=felsenstein: a correction introduced by Joe Felsenstein
that allows to explicitely specify the number of invariable sites
(if known) one wants to correct for.
--asc-corr=stamatakis: a correction introduced by myself that
allows to explicitely specify the number of invariable sites for
each character (if known) one wants to correct for.
H.."">
Example:raxmlHPC -p 12345 -s alg -n TEST -m ASC_GTRGAMMA –asc-corr=lewis
."."""<2
.
.("!"
."!!".5felsestein
(7"!3"!""".5stamatakis
(798""!"
!"!.""8
43
".
1.""..!
!"(5felsenstein7.!(!
"(5stamatakis7(I8"!
(8("!(I-q(
!
Example 2:raxmlHPC -p 12345 -s alg -n TEST -m ASC_GTRGAMMA
--asc-corr=stamatakis -q part
Example 3:raxmlHPC -p 12345 -s alg -n TEST -m ASC_GTRGAMMA
--asc-corr=felsenstein -q part
R.8.(!"(I>
[asc~p1.txt], ASC_DNA, p4=1-1000
[asc~p2.txt], ASC_DNA, p5=1001-1965
8I"8(!I"
"!3"!"((I"p1.txt
p2.txt98("I("asc.
~(G
8"(".I""
11""8I">
(%>
1000
(>
2000
).8I(""!1000
8.!"(""!2000
98"I5p1.txtp2.txt7"
"(G
1""8I"!.!-9>
(%>
250 300 400 100
(>
500 300 200 200
).!I(""!250
"!8300"!/8400!'100 !1
"(""!500!8300/8200 '
200
M"."".:1H""..
.8"(8.""!
"!%$$$I(""!/'
"""..."!3"!
44
(
WARNING: )"""I58p1.txt
p2.txt7!""(("!
"(!!3"!(>
BINARY: 0,1
DNA: A, C, G, T
PROTEIN: A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V
--flag-check When using this option, RAxML will only check if all command line
flags specifed are available and then exit with a message listing
all invalid command line flags or with a message stating that all
flags are valid.
(!#(.((!. .!
""!!"(
(.B6"!AN.
(((
Example 1: raxmlHPC --flag-check -f a -s alg -p 12345 -N 20 -x 12345
-m GTRGAMMA -n T1
Output: All options supported
Example 2: raxmlHPC --flag-check -f a -s alg -p 12345 -N 20 -x 12345
-m GTRGAMMA --nonsense-option -n T1
Output: Option --nonsense-option not supported
--auto-prot=ml|bic|aic|aicc When using automatic protein model selection you can
chose the criterion for selecting these models. RAxML will test all
available prot subst. models except for LG4M, LG4X, and GTR-based models
with and without empirical base frequencies.
You can chose between ML score based selection and the BIC, AIC, and AICc
criteria.
DEFAULT: ml
Example: raxmlHPC -s alg -p 12345 -m PROTGAMMAAUTO --auto-prot=bic -n T1
".".(R !
/
1!.(!("
(!5.jplace (I!E<7.I8.(!!
"(((>
(>AA...(A"A!S#S1%$%#X%S1B($$#%$$Q
--epa-keep-placements=number specify the number of potential placements you want
to keep for each read in the EPA algorithm .
Note that, the actual values printed will also depend on the settings for
--epa-prob-threshold=threshold !
45
DEFAULT: 7
Example: raxmlHPC -f v --epa-keep-placements=100 -t tree -m GTRCAT -s alg
-n T1
8.(%$$(" .jplace ("I8
(! --epa-prob-threshold.
--epa-prob-threshold=threshold specify a percent threshold for including potential
placements of a read depending on the maximum placement weight for this
read. If you set this value to 0.01 placements that have a placement weight
of 1 per cent of the maximum placement will still be printed to file if the
setting of --epa-keep-placements allows for it
DEFAULT: 0.01
Example: raxmlHPC -f v –epa-prob-threshold=0.05 -t tree -m GTRCAT -s alg
-n T1
8.((" .jplace ("I
.!PS!!(".!("I"
!!("(("IWepa-keep-placements
"
--epa-accumulated-threshold=threshold specify an accumulated likelihood weight
threshold for which different placements of read are printed to file.
Placements for a read will be printed until the sum of their placement
weights has reached the threshold value.
Note that, this option can neither be used in combination with
--epa-prob-threshold nor with --epa-keep-placements!
Example: raxmlHPC -f v --epa-accumulated-threshold=0.95 -t tree -m GTRCAT -s
alg -n T1
8.(("! .jplace ("I
""."!$QP5!!%$7
--JC69 specify that all DNA partitions will evolve under the Jukes-Cantor model,
this overrides all other model specifications for DNA partitions.
DEFAULT: Off
Example: raxmlHPC -p 12345 -m GTRGAMMA -s alg --JC69 -n T1
--K80 specify that all DNA partitions will evolve under the K80 model, this
overrides all other model specifications for DNA partitions.
DEFAULT: Off
98(!(.8"I!
8"!O'/O.
%$988"
[57.
46
Example: raxmlHPC -p 12345 -m GTRGAMMA -s alg --K80 -n T1
--HKY85 specify that all DNA partitions will evolve under the HKY85 model, this
overrides all other model specifications for DNA partitions.
DEFAULT: Off
98(!(.8"I!
8"!O'/O.
%$988"
[57.
Example: raxmlHPC -p 12345 -m GTRGAMMA -s alg --HKY85 -n T1
--set-thread-affinity specify that thread-to-core affinity shall be set by RAxML
for the hybrid MPI-PThreads version
DEFAULT: Off
=(!< *<!
""""((."2
.8((G H!
!.M"< *<"G
Example:raxmlHPC-HYBRID -m GAMMA -s alg -p 12345 -N 20 --set-thread-affinity
-n T1
--bootstop-perms=number specify the number of permutations to be conducted for the
bootstopping/bootstrap convergence test. The allowed minimum number is 100!
DEFAULT: 100
=.%$$$"!
(""AL""!!
((.M..
""!(
Example:raxmlHPC -B 0.02 --bootstop-perms=1000 -b 12345 -p 12345 -# AUTOMR
-s alg -m GTRCAT -n TEST
--quartets-without-replacement specify that quartets are randomly subsampled, but
without replacement.
DEFAULT: random sampling with replacements
Example:raxmlHPC -s alg -p 12345 -m GTRGAMMA -f q -N 50 --quartets-without-
replacement -n TEST
IX. Output Files
-("(..!(I
(I8-n exampleRun..8.
"!(I((8
47
.(I!(!.">
ls *exampleRun*
RaxML_info.exampleRun: "!.
. " I '* 57 . ( (
(57 ( I 8 ! .
"5-i 7!
(."
This is the most important output 8le ".
..("!"( "!
(I..
RAxML_log.exampleRun:I(8!"
!""(I5!!""(("I7!"
!" "I!
I(I.!(("8*#
-b("I "!(!"5-#
(7*1""
RAxML_result.exampleRun:/I(!"I
.!"!"8"".
-t " "(" I . ! ((
"8 -#-b("I
RAxML_parsimonyTree.exampleRun: " 6 ( !
((-t..8I..
!(("-#-b(
RAxML_randomTree.exampleRun: ""(!(
.".-d
RAxML_checkpoint.exampleRun.checkpointNumber: < ! ("I -j
""(./"(!$.
! ! " 8 ""( I
!(!"("I -#
)!""(I.(("
RAxML_bootstrap.exampleRun: !((" -# -b -x I
((..8I
RAxML_bipartitions.exampleRun: !-f b(8I."(
."I"!$%$$.G (.*f a -x
("I8!(..R((
!"
RAxML_bipartitionsBranchLabels.exampleRun: / ! I
8((""(9.""
GSupport values always refer to branches/splits of trees and never to nodes
of the tree.98.(("8
.(!9."!
48
RAxML_bipartitionFrequencies.exampleRun: /(*.(!3"!
"I(-t -z.-f m(
RAxML_perSiteLLs.exampleRun:/(W"(66!
! . /29E 5(>AA...""B(A\A(A"A7 I
(.-f g("I
RAxML_bestTree.exampleRun:/*"!
RAxML_distances.exampleRun: / (*. * " . *
(I(.-f x (
X. Computing TC and IC values
!. ((!"( //"!
"$%#(>AA..."A(A#&PXP
"!.(( ..">
(>AA!BA"AA$%@A$A$XA$&%" (D!0B
D &P1'9$62.
8!$)"""/A /""""!(
"" . (( ! ( " (( >
(>AAA%$%%$%A$$P#
Warning: !/A /""""RE
(( " . " ((8 ( I
bipartitionList.c"#define BIP_FILTER
. ( ! . M !
"((""! //")
"N" (8 ! "" !
"( /"8!3""!3"!PS
.""!!"!"N"(8.
(" !" ( "N" . " 8 !"
"( . " 8 ! (
"N".!"("(."
"" /"8(.(""" /
"3/"((8".
""N"""N"! "(
(
'!8""""B"5
7.B"5E7
58"7(" / /
"
1"8"( /8 /8/8/"!!/
.(>
raxmlHPC -L MR -z 1070_yeast_genetrees.tre -m GTRCAT -n T1
.
-L MR("I".("(
49
-z 1070_yeast_genetrees.tre("II"!
5."!%8$X$6"8
$%#8."((("(7
-m GTRCAT 5.M".8
3(7
-n T1 -(((I
."8. / /"8(
(IRAxML_MajorityRuleConsensusTree_IC.T18.".>
(Scer,Spar,(Smik,(Skud,(Sbay,(Scas,(Cgla,(Kpol,(Zrou,((Clus,((Psti,((Ctro,
(Calb,Cdub):1.0[0.95,0.95]):1.0[0.77,0.77],
(Cpar,Lelo):1.0[0.76,0.76]):1.0[0.75,0.75]):1.0[0.11,0.11],
(Cgui,Dhan):1.0[0.02,0.07]):1.0[0.02,0.08]):1.0[0.97,0.97],((Sklu,
(Kwal,Kthe):1.0[0.97,0.97]):1.0[0.32,0.23],
(Agos,Klac):1.0[0.08,0.08]):1.0[0.04,0.10]):1.0[0.59,0.47]):1.0[0.02,0.02]):1.0[0.1
1,0.11]):1.0[0.02,0.02]):1.0[0.97,0.97]):1.0[0.05,0.14]):1.0[0.30,0.27]):1.0[0.54,0
.54]);
1 " " ! "" 8 .
length[x,y] "8.length"("5"E
8" 1.0!78x"(
/"y /"
.""//"!8.//
"6(//"!!!"
!!
"((RAxML_info.runID(I
".5"RAxML_info.T17.>
Tree certainty for this tree: 7.642240
Relative tree certainty for this tree: 0.382112
Tree certainty including all conflicting bipartitions (TCA) for this tree: 7.580023
Relative tree certainty including all conflicting bipartitions (TCA) for this tree: 0.379001
'!8""""
58"7(" / /"
(""(*!"!/5I(
/ 8 !"8 9<*[ <(8 ). %QQ&7 ; ! (
(!<!8(.(
"( /8 /8/8/".(>
raxmlHPC -L MRE -z 1070_yeast_genetrees.tre -m GTRCAT -n T2
" "( 8 ! !" (
A!"(""(".
.P%%$$S1"8(
raxmlHPC -L T_75 -z 1070_yeast_genetrees.tre -m GTRCAT -n T3
.( /8 /8//""(
]XPS((
50
)((5-f i7.""( /8 /8
/8/"8"!"!"5!(8*.
7
-f b(.(((!
!(!"(("(
raxmlHPC -f i -t yeast_concatenationtree.tre -z 1070_yeast_genetrees.tre -m GTRCAT -n T4
98"Iyeast_concatenationtree.tre"!"
"" (8yeast_concatenationtree.treI*
."""!%8$X$
!((
+"8.yeast_concatenationtree.tre. /
/"8((IRAxML_IC_Score_BranchLabels.T48."
.>
(((((((Clus:0.47168135428609103688((((Lelo:0.30356174702769450624,Cpar:0.2549087423
9480920682):0.13023178275857649755[0.76,0.76],
(Ctro:0.18383414558272206940(Calb:0.04124660275465741321,Cdub:0.0429080158839683228
9):0.14526604486383792869[0.95,0.95]):0.12355825028654655873[0.77,0.77]):0.17335821
030783615804[0.75,0.75],Psti:0.42255112174261910685):0.07862882822310976461[0.11,0.
11],
(Cgui:0.45961028886034632768,Dhan:0.28259245937168109286):0.05586015476156453580[0.
02,0.07]):0.08116340505230199009[0.02,0.08]):1.03598510402913923656[0.97,0.97],
((Agos:0.53332956655591512440,Klac:0.47072785596320687596):0.08132006357704427146[0
.08,0.08],
((Kthe:0.17123899487739652203,Kwal:0.17320923240031221857):0.25620117495110567019[0
.97,0.97],Sklu:0.24833228915799765435):0.05646992617871094550[0.32,0.23]):0.0523630
6187235122145[0.04,0.10]):0.10686517691208799463[0.59,0.47],Zrou:0.4130783368556378
2877):0.03792570537296727218[0.02,0.02],Kpol:0.43287284049576529865):0.045603416931
36910068[0.11,0.11],Cgla:0.49584136365135367264):0.04363310339731014259[0.02,0.02],
Scas:0.37212829744050218705):0.29362133996280515014[0.97,0.97],
(Skud:0.06926467973344750673,(Smik:0.06535810850036427588,
(Scer:0.04285848856634000975,Spar:0.03030513540244994877):0.02506719066056842596[0.
54,0.54]):0.02459323291555862850[0.30,0.27]):0.02524223867026276907[0.05,0.14],Sbay
:0.06506923220637816918);
1""!(.length[x,y] "
8.length"("((-t8 x
"( /"y /".(//"!
(RAxML_info.T4(I".
! / /"("8"8
"!(((8!"A(A(!
.!"
E".58-"((>AA!*A!.A"(A7"
(((9."!("
!( / /"8.
(( . * 8 ." .
"** /"** /""
)"" / /".. / /"
!"""(".
(("N"( "8.( / /"
51
!.
18 . ( ( ( . ! "6
(""N"(
,"-C "."!(
. . ( ! ( I> 2 ! I
""("("N"(9."!
5" RAxML_verboseIC.runID.0 … RAxML_verboseIC.runID.N-18 . N !
(7(I(5""N"7
<= <*!5"RAxML_verboseSplits.runID7
1(8-C("
raxmlHPC -f i -t yeast_concatenationtree.tre -z 1070_yeast_genetrees.tre -m GTRCAT -n T5 -C
. (" $ I 5 ! " ! $ ( (
yeast_concatenationtree.tre7 RAxML_verboseIC.T5.0, RAxML_verboseIC.T5.1, …,
RAxML_verboseIC.T5.19
1(8RAxML_verboseIC.T5.0I.>
((Cpar, Lelo),(Scer, Smik, Skud, Cgla, Kpol, Zrou, Kwal, Kthe, Agos, Klac, Clus,
Cgui, Psti, Ctro, Calb, Cdub, Dhan, Sklu, Scas, Sbay, Spar));
((Cpar, Ctro, Calb, Cdub),(Scer, Smik, Skud, Cgla, Kpol, Zrou, Kwal, Kthe, Agos,
Klac, Clus, Cgui, Psti, Lelo, Dhan, Sklu, Scas, Sbay, Spar));
. I 9." ( ( . "
yeast_concatenationtree.tre !. 9." ( "(
"N"("!!3"! """ "!
RAxML_verboseIC.T5.0 I I (8 ." "
yeast_concatenationtree.tre "N" . (8 ."
"(
8( I ( 5" "N"7 <= <*
!5RAxML_verboseSplits.T578>
1. Scer
2. Smik
3. Skud
4. Cgla
5. Kpol
6. Zrou
7. Kwal
8. Kthe
9. Agos
10. Klac
11. Clus
12. Cgui
13. Psti
14. Cpar
15. Lelo
16. Ctro
17. Calb
18. Cdub
19. Dhan
52
20. Sklu
21. Scas
22. Sbay
23. Spar
partition:
----- ----- ---** ----- --- 956/89.345794/0.761406
----- ----- ---*- ***-- --- 39/3.644860/0.761406
partition:
----- ----- ----- -**-- --- 1051/98.224299/0.949483
----- ----- ----- **--- --- 6/0.560748/0.949483
.
.
.
partition:
--*** ***** ***** ***** **- 641/59.906542/0.303620
-**-- ----- ----- ----- -*- 148/13.831776/0.303620
-*-** ***** ***** ***** *-- 114/10.654206/0.303620
partition:
-**** ***** ***** ***** **- 825/77.102804/0.545775
-**-- ----- ----- ----- -** 87/8.130841/0.545775
"".(."("I"(
"("N"("
x/y/z""(!3"!(5x78((("5
.((!3"[y78 /"5z7
XI. Simple RAxML Analyses
.*8."".!(*."
8(ex_al
()
!.!. 65
%8$$$7""!R("
(R"."
.""!88"!R(""!
W"
BR".(>
raxmlHPC -x 12345 -p 12345 -# 100 -m GTRGAMMA -s ex_al -n TEST
(""">
raxmlHPC -x 12345 -p 12345 -# autoMRE -m GTRGAMMA -s ex_al -n TEST
. "" ( (( " ' !
9.8!.!88R"(>
53
raxmlHPC -f a -x 12345 -p 12345 -# 100 -m GTRGAMMA -s ex_al -n TEST
.I""R"""!W"
"(.((5RAxML_bootstrap.TEST78"
5RAxML_bestTree.TEST7R((.*"
5RAxML_bipartitions.TEST7 . 8 "" " (( !
""5RAxML_bipartitionsBranchLabels.TEST7
188 "!R(" -# .
"8"!(6PR(
"!
)-# autoMRE ("I."!%$$$R(""8
8!""
1. !8.".
$ " " ! . ^ %8$$$
3"
1.."""".8
B
Warning: (R"."""
I(-t-z
.8""(5-g -r7..(R
!(7
-(!((R"
..("""8(((
! !"! -m GTRCAT
! ( -q partitionFileName ! !.
"
: "* 7
! ; ("! . -i ( ( .
"*(6< .
((6.!P8%$8%P8
$8P(.
("".>
185$P7(...
"
54
"8(!"
(""5
".%8Q$$7
!8 "( ! 5 7 . "
!.(*I!%$."(
L"L"("""
(...PI;I"(
!6<
9.("!8!.
."(<. -y (98.(
M-p"G
raxmlHPC -y -p 12345 -s ex_al -m GTRCAT -n ST0
...
raxmlHPC -y -p 34556 -s ex_al -m GTRCAT -n ST4
8!!I -i 10
raxmlHPC -f d -i 10 -m GTRCAT -s ex_al -t RAxML_parsimonyTree.ST0 -n FI0
...
raxmlHPC -f d -i 10 -m GTRCAT -s ex_al -t RAxML_parsimonyTree.ST4 -n FI4
">
raxmlHPC -f d -m GTRCAT -s ex_al -t RAxML_parsimonyTree.ST0 -n AI0
...
raxmlHPC -f d -m GTRCAT -s ex_al -t RAxML_parsimonyTree.ST4 -n AI4
I " " "(
'!!3
: @>
!"-"!(
I""!"".
'/!I*.
!((
8(."(!-c."
'*
((("!"
.!
= * . " *" " ! %P
"
raxmlHPC -f d -c 10 -m GTRCAT -s ex_al -t RAxML_parsimonyTree.ST0 -n C10_0
...
raxmlHPC -f d -c 10 -m GTRCAT -s ex_al -t RAxML_parsimonyTree.ST4 -n C10_4
=;.!!-c 25"8"
55
"".
raxmlHPC -f d -c 40 -m GTRCAT -s ex_al -t RAxML_parsimonyTree.ST0 -n C40_0
...
raxmlHPC -f d -c 40 -m GTRCAT -s ex_al -t RAxML_parsimonyTree.ST4 -n C40_4
!
"'/((.""(.(((
!-c 25
.8(" -c 25 . %Q *. ( -c 55
L"8"(!""!I''
!(.""
8! -c"I''
!;"((. -c-i
" -i ".("I
8 " ! " " ("
" 18 ! . " !
!(""
!"!( -c
" " ! I
RAxML_info.AI_0 ... RAxML_info.AI_4
) 0A%&/A%2
6(.(
."*(66
(.3"!)3"
"(!5"(*!7
.I"!$"!(<"
""(6<"9:59:7
( 8 ! .
((6!(!"(
(""(""
!8I!"
."!I(!"
R"(I"
! . 5( " "7 "
= " -f r ( "( (. (" *1 "
.!
8!L""("8((8
( !" 5 " $$ !" " *. .
R7.
2("...-d(
56
!"(!.("(
.-#(.(< </*< "(
8"(!"("B(>
raxmlHPC -f d -p 12345 -m GTRCAT -s ex_al -# 10 -n MultipleOriginal
!".("!>
raxmlHPC-MPI -f d -m GTRCAt -p 12345 -s ex_al -# 100 -n MultipleOriginal
("("< *"8 mpiexec mpirun(
"5("".""("7
*+%
"(*("(.3!B(>
raxmlHPC -f d -m GTRCAT -s ex_al -p 12345 -# 100 -b 12345 -n MultipleBootstrap
=("!! -b !!
(-p!!(..
("
(((>
raxmlHPC-MPI -f d -m GTRCAT -s ex_al -# 100 -p 12345 -b 12345 -n MultipleBootstrap
"("(((< ""
9> B
(("$$!"%8$$$(
=".-f b(.!!%8$$$((
((.((1(!.
.*"!$$
((8 *".! QQ("I
"RAxML_result.MultipleOriginal.RUN.99
! " ( . 3 !
" "(8 %$ . %$$ ( %$ " . I
"" *( I ! ( I "
RAxML_bootstrap.MultipleBootstrap.0...RAxML_bootstrap.MultipleBootstrap.9 "
"" 9+A+9 cat "8
cat RAxML_bootstrap.MultipleBootstrap.* > RAxML_bootstrap.All
.(B"".>
raxmlHPC -f b -m GTRCAT -z RaxML_bootstrap.All -t RAxML_result.MultipleOriginal.RUN.99 -n BS_TREE
.(-t (("
.(.(.8("
!*8""*8!(
="."(B"!((">
57
raxmlHPC -J MR -m GTRCAT -z RaxML_bootstrap.All -n MR_CONS
B">
raxmlHPC -J MRE -m GTRCAT -z RaxML_bootstrap.All -n MRE_CONS
">
raxmlHPC -J STRICT -m GTRCAT -z RaxML_bootstrap.All -n STRICT_CONS
1I" -J STRICT_DROP -J MR_DROP (
".*(>(>AA*A
XII. A Simple Heterotachous Model
)(("'
"!"'"!
."((.8H..
( " ( ( ( ! ' !
!3""(
!.'(6.("!
"(6("
""3!
!6-93"'!G
" ." ! 8 . "(
-D_HET CFLAGS =("I8.
("!-m GTRGAMMA""".""
"
Z(8."8'"((""
!%$!(!!P!'
2("I.
XIII. Frequently Asked Questions
Q: )(! ("(8(!
58
"*(*(88*(.(
C
A: " ) (! R( ( 8 ((
. ( ! . (8 8 (( (
" " ! "
(
Q: / 9E+*(I!.C
A: 9 "8 " 1 ZM 5!M_*7 + !
Z."(.(("<="(
I(("(I"*(!
=".(>AA...6A.A
Q: );((! 5<* 78(!"
(C
A: (<* ((8
.
3 3"(
>><>008
" " ! !
("<* 8''8'/8<*
("((""(8("(
"" ! ( M "
( "" ! <* " .
'" 0 M"""!<* "
'".(88(<*
"(6(!"8"I"
( ( 5 "( (7
(6(" !"8 . .(<*
(( "8 .*. "
("( H3J=!$$
(!>
" C:=
=D
J/("E52*
!+<8$$&7[3!(%%#W%%@>
&"C:>D
>E
= > >
6=& >>>D
"8 !"L"..!!.
(" ( . " ! R8 . .
''!.('U`U
Q: )('*!"C
A: 1""!"(8(6
! !" ' "
!*.-98L"(
59
(6!M(!"."("
"!'("L".
3 (.('
.(""("8("(<
"Modeltest ((!(!("I"!
!I((I".
'("'.
( 8"
!!"!!*(6"
"(.<".
( L" ( L"
"(!B(""!'
18 (( ! (
(" " (" I 3
8L"(!("""
(
Q: )(!"!*.C
A: >-(3!!
(!" ! " " !
!"
1(8!."(!(
"""."3"
(*I.""
("8..(H..3"
(I".(8"
""(*I("
"
88"
M"!!M!"
("8""I"5!"PW%$7
("""((8
!""!99 "599 7
.8"!!
.!
(((!""
8( ("W1"
"!"(!".((!
.
!.""(!""
..""
(""(
8 (( . !
!""("!.
("
(.!R"
"I"I"(!(
Q: ) .!< C
A: =(!("!-#-N("*."
!< .((
60
Q: )(8" (!"(
B8.RC
A: /8(!"((.8.
" " . . A "
(""(
Q: .(
A: *((
""8(N !..:
1H" .(..
(
Q: ) "(".
A: .8(!
3".".H."!"
61
