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_raxml
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#compdef raxml raxmlHPC -P raxmlHPC-*
_raxml() {
local ret=1
local -a args
args+=(
'-a+[Specify a column weight file]:file:_files'
'-A+[Specify one of the secondary structure substitution models]:model:(S6A S6B S6C S6D S6E S7A S7B S7C S7D S7E S7F S16 S16A S16B)'
'-b+[Specify an integer number (random seed) and turn on bootstrapping]:int:'
'-B+[cutoff threshold for the MR-based bootstopping criteria]:float:'
'-c+[Specify number of distinct rate catgories]:int:'
'-C[Enable verbose output for the "-L" and "-f i" options]'
'-d[start ML optimization from random starting tree]'
'-D[ML search convergence criterion]'
'-e+[Set model optimization precision in log likelihood units]:float:'
'-E+[Specify an file that contains a specification of alignment positions you wish to exclude]:file:_files'
'-f+[Select algorithm]:algorithm:((
a\:rapid\ Bootstrap\ analysis\ and\ search\ for\ best-scoring\ ML\ tree\ in\ one\ program\ run
A\:compute\ marginal\ ancestral\ states\ on\ a\ ROOTED\ reference\ tree
b\:draw\ bipartition\ information\ on\ a\ tree\ based\ on\ multiple\ trees
B\:optimize\ br-len\ scaler\ and\ other\ model\ parameters
c\:check\ if\ the\ alignment\ can\ be\ properly\ read\ by\ RAxML
C\:ancestral\ sequence\ test\ for\ Jiajie
d\:new\ rapid\ hill-climbing
D\:rapid\ hill-climbing\ with\ RELL\ bootstraps
e\:optimize\ model+branch\ lengths\ under\ GAMMA/GAMMAI\ only
E\:execute\ very\ fast\ experimental\ tree\ search
F\:execute\ fast\ experimental\ tree\ search
g\:compute\ per\ site\ log\ Likelihoods\ with\ model\ estimate\ from\ first\ tree
G\:compute\ per\ site\ log\ Likelihoods\ with\ model\ reestimated\ for\ each\ tree
h\:compute\ log\ likelihood\ test\ (SH-test)\ between\ trees
H\:compute\ log\ likelihood\ test\ (SH-test)\ between\ trees\ with\ model\ reestimated\ for\ each\ tree
i\:calculate\ IC\ and\ TC\ scores
I\:a\ simple\ tree\ rooting\ algorithm\ for\ unrooted\ trees
j\:generate\ a\ bunch\ of\ bootstrapped\ alignment\ files
J\:Compute\ SH-like\ support\ values
k\:Fix\ long\ branch\ lengths\ in\ partitioned\ data\ sets
m\:compare\ bipartitions\ between\ two\ bunches\ of\ trees
n\:compute\ the\ log\ likelihood\ score\ of\ all\ trees
N\:compute\ the\ log\ likelihood\ score\ of\ all\ trees\ with\ model\ reestimated\ for\ each\ tree
o\:old\ and\ slower\ rapid\ hill-climbing\ without\ heuristic\ cutoff
p\:perform\ pure\ stepwise\ MP\ addition
P\:perform\ a\ phylogenetic\ placement
q\:fest\ quartet\ calculator
r\:compute\ pairwise\ Robinson-Foulds\ (RF)\ distances
R\:compute\ all\ pairwise\ Robinson-Foulds\ (RF)\ distances
s\:split\ up\ a\ multi-gene\ partitioned\ alignment
S\:compute\ site-specific\ placement\ bias
t\:do\ randomized\ tree\ searches
T\:do\ final\ thorough\ optimization\ of\ ML\ tree
u\:execute\ morphological\ weight\ calibration
v\:classify\ a\ bunch\ of\ environmental\ sequences
V\:classify\ a\ bunch\ of\ environmental\ sequences\ \(experimental\)
w\:compute\ ELW\ test
W\:compute\ ELW\ test\ with\ model\ re-estimated\ for\ each\ tree
x\:compute\ pair-wise\ ML\ distances
y\:classify\ a\ bunch\ of\ environmental\ sequences\ using\ parsimony
))'
'-F[enable ML tree searches under CAT model]'
'-g+[specify the file name of a multifurcating constraint tree]:file:_files'
'-G+[enable the ML-based evolutionary placement algorithm heuristics]:float:'
'(- *)-h[display help message]'
'-H[Disable pattern compression]'
'-i+[Initial rearrangement setting]: :'
'-I+[a posteriori bootstopping analysis]:algorithm:((
autoFC\:frequency-based\ criterion
autoMR\:majority-rule\ consensus\ tree\ criterion
autoMRE\:extended\ majority-rule\ consensus\ tree\ criterion
autoMRE_IGN\:metrics\ similar\ to\ MRE,\ but\ include\ bipartitions\ under\ the\ threshold
))'
'-j+[Specifies intermediate tree files]:file:_files'
'-J+[Tree computation option]:algorithm:((
MR\:majority\ rule\ consensus\ tree
MRE\:extended\ majority\ rule\ consensus\ tree
STRICT\:strict\ consensus\ tree
STRICT_DROP\:identifies\ dropsets
MR_DROP\:identifies\ dropsets
T_\<PERCENT\>\:specify\ percent
))'
'-k[Printed bootstrapped trees with branch lengths]'
'-K+[Specify a multi-state substitution models]:model:(ORDERED MK GTR)'
'-L+[Compute consensus trees labelled by IC supports]:strategy:(MR MRE T_NUM)'
'-m+[Specify substitution model]:model:(
BINCAT BINCATX BINCATI BINCATIX ASC_BINCAT ASC_BINCATX
BINGAMMA BINGAMMAX ASC_BINGAMMA ASC_BINGAMMAX BINGAMMAI BINGAMMAIX
GTRCAT GTRCATX GTRCATI GTRCATIX ASC_GTRCAT ASC_GTRCATX
GTRGAMMA GTRGAMMAX ASC_GTRGAMMA ASC_GTRGAMMAX
GTRGAMMAI GTRGAMMAIX
MULTICAT MULTICATX MULTICATI MULTICATIX
ASC_MULTICAT ASC_MULTICATX MULTIGAMMA MULTIGAMMAX
ASC_MULTIGAMMA ASC_MULTIGAMMAX MULTIGAMMAI MULTIGAMMAIX
PROTCAT
PROTCATI
ASC_PROTCAT
PROTGAMMA
ASC_PROTGAMMA
PROTGAMMAI)' # TODO: if anyone really cares, this can be heavily improved
'-M[Switch on estimation of individual per-partition branch lengths]'
'-n+[Specifies the name of the output file]:file:_files'
'-o+[Specify the name of a outgroup]:str:'
'-O[Disable check for completely undetermined sequence in alignment]'
'-p+[Specify a random number seed for the parsimony inferences]:int:'
'-P+[Specify a user-defined AA substitution model]:file:_files'
'-q+[Specify the assignment of models to alignment partitions]:file:_files'
'-r+[Specify the file name of a binary constraint tree]:file:_files'
'-R+[Specify the file name of a binary model parameter]:file:_files'
'-s+[Specify the alignment data file in PHYLIP format]:file:_files'
'-S+[Specify the name of a secondary structure file]:file:_files'
'-t+[Specify a user starting tree file in Newick format]:file:_files'
# TODO: PTHREADS VERSION ONLY
'-T+[Specify the number of threads you want to run]:int:'
'-u[use the median for the discrete approximation of the GAMMA model of rate heterogeneity]'
'-U[Try to save memory by using SEV-based implementation for gap columns ]'
'-v[Display version information]'
'-V[Disable rate heterogeneity among sites model]'
'-w+[FULL path to the directory into which RAxML shall write its output files]:dir:_files -/'
'-W+[Sliding window size]:int:'
'-x+[Seed for rapid bootstrapping]:int:'
'-X[Superficial version of -y]'
'-y[Compute only a parsimony starting tree with RAxML]'
'-Y[File name defining four groups from which to draw quartets]:file:_files'
'-z+[file containing multiple trees that shall be used to draw bipartition values]:file:_files'
{-\#,-N}'+[Specify the number of alternative runs on distinct starting trees]:int:'
'--mesquite[Print output files that can be parsed by Mesquite]'
'--silent[Disables printout of warnings]'
'--no-seq-check[Disables checking the input MSA for identical sequences and undetermined sites]'
'--no-bfgs[Disables automatic usage of BFGS method]'
'--asc-corr=[Specify the type of ascertainment bias correction you wish to use]:type:(lewis felsenstein stamatakis)'
'--flag-check[only check if all command line flags specifed are available and then exit]'
'--auto-prot=[Change the criterion for automatic protien model selection]:criterion:(ml bic aic aicc)'
'--epa-keep-placements=[Specify the number of potential placements you want to keep]:number:'
'--epa-prob-threshold=[Specify a percent threshold for including potential placements]:number:'
'--epa-accumulated-threshold=[Specify an accumulated likelihood weight threshold]:number:'
'(--JC69 --K80 --HKY85)--JC69[All DNA patitions will evolve under Jukes-Cantor model]'
'(--JC69 --K80 --HKY85)--K80[All DNA patitions will evolve under K80 model]'
'(--JC69 --K80 --HKY85)--HKY85[All DNA patitions will evolve under HKY85 model]'
'--asc-miss=[Specify the fraction of missing data]:number:'
'*:file:_files'
)
_arguments -w -s -S $args[@] && ret=0
return ret
}
_raxml