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_fasttree
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#compdef fasttree
# This does not include all available options, but the FastTree help
# is too messy for me to figure out how to use it.
_fasttree() {
integer ret=1
local -a args
args+=(
"-n[read in multiple alignments]:number:"
"(-intree1)-intree[read the starting tree in from newickfile]:file:_files"
"(-intree)-intree1[read the same starting tree for each alignment]:file:_files"
"(-nopr)-quiet[do not write to standard error during normal operation]"
"(-quiet)-nopr[do not write the progress indicator to stderr]"
"-log[save intermediate trees]:file:_files"
"-quote[quote sequence names in the output]"
"-matrix[specify amino acid dissimilarity matrix]:file:_files"
"-rawdist[turn the log-correction off or use %different instead of Jukes-Cantor]"
"-pseudo[pseudocounts to estimate distances]::weight:"
"-nni[the number of rounds of min. evo. NNIs]:number:"
"-spr[the rounds of SPRs]:number:"
"(-mllen -mlnni)-noml[turn off both min-evo NNIs and SPRs]"
"(-noml -mlnni)-mllen[optimize branch lengths without ML NNIs]"
"(-noml -mllen)-mlnni[number of rounds of maximum-likelihood NNIs]:number:"
"-sprlength[the maximum length of a SPR move]:number:"
"-mlacc[always optimize all 5 branches at each NNI]:number:"
"-slownni[turn off heuristics to avoid constant subtrees]"
"-wag[Whelan-And-Goldman 2001 model]"
"-gtr[generalized time-reversible model]"
"(-nocat)-cat[rate categories of sites]:number:"
"(-cat)-nocat[no CAT model]"
"-gamma[report the likelihood under the discrete gamma model]"
"-nome[minimum-evolution bootstrap supports]"
"-nosupport[turn off support values]"
"-boot[number of bootstrap resamples]:number:"
"-seed[initialize the random number generator]:number:"
"(-fastest -notop)-slow[exhaustive search]"
"(-slow -2nd)-fastest[search the visible set only]"
"-notop[don't speed up the search via top-hit list]"
"-topm[set the top-hit list size to parameter*sqrt(N)]:number:"
"-close[the close heuristic, lower is more conservative]:number:"
"-refresh[join node comparison threshold]:number:"
"(-no2nd)-2nd[enable 2nd-level top hits heuristic]"
"(-2nd)-no2nd[disable 2nd-level top hits heuristic]"
"(-bionj)-nj[regular (unweighted) neighbor-joining]"
"(-nj)-bionj[weighted joins as in BIONJ]"
"-constraints[an alignment with values of 0, 1, and -]:file:_files"
"-constraintWeight[how strongly to weight the constraints]:number:"
"*:file:_files"
)
_arguments $args[@] && ret=0
return ret
}
_fasttree