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.

SEE ALSO

       See                                    documentation                                    at
       https://github.com/blackrim/phyutility/blob/master/manual.pdf?raw=true      for       more
       information.

AUTHOR

       Stephen A. Smith http://www.blackrim.org eebsmith@umich.edu