phyutility - Online in the Cloud

PROGRAM:

NAME

phyutility - tools for manipulating sequences and phylogenies

SYNOPSIS

phyutility <command> <options>

DESCRIPTION

Phyutility is a command line program that performs simple analyses or modifications on
both trees and data matrices.

OPTIONS

To get help on a specific command use option -h <command>

COMMANDS
for trees:

consensus
Calculate consensus trees. Use like -con -t <threshold> -in <infile> -out
<outfile>.

convert
Convert tree files. Use like -vert -in <infile> -out <outfile>.

leafstab
Leaf stability index calculation. Use like -ls -in <infile>.

linmove
Lineage movement calculation. Use like -lm -names <tip names> -tree <consensus>
-in <infile> -out <outfile>.

prune
Prune lineages. Use like -pr -names <tip names> -in <infile> -out <outfile>.

reroot
Reroot trees. Use like -rr -names <tip names> -in <infile> -out <outfile>.

thin
Thin trees. Use like -tt # -in <infile> -out <outfile>.

treesupp
Support for a set of trees. Use like -ts -tree <tree> -in <infile> -out <outfile>.

for seqs:

clean
Trim seqs based on threshold. Use like -clean # -in <infile> -out <outfile> -aa
<to force aa>.

concat
Concatenate alignments. Use like -concat -in <infiles> -out <outfile> -aa <to
force aa>.

ncbiget
Fetch seqs from NCBI. For options run phyutility -h ncbiget.

ncbisearch
Seach NCBI. For options run phyutility -h ncbisearch.

parse
Parse genbank results. For options run phyutility -h parse.

EXAMPLE

phyutility -con -t 0.5 -in testall.tre -out test.con
Consensus the set of trees in testall.tre collapsing branches with less than 0.5
frequency.

phyutility -vert -in test.tre -out testvert.nex
Convert the tree file from newick in test.tre into nexus in testvert.nex.

phyutility -concat -in test.aln test2.aln -out testall.nex
Concatenate 2 alignment files into nexus in testall.nex.

Use phyutility online using onworks.net services