EnglishFrenchSpanish

OnWorks favicon

phyutility - Online in the Cloud

Run phyutility in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command phyutility that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    strace
    strace
    The strace project has been moved to
    https://strace.io. strace is a
    diagnostic, debugging and instructional
    userspace tracer for Linux. It is used
    to monitor a...
    Download strace
  • 2
    gMKVExtractGUI
    gMKVExtractGUI
    A GUI for mkvextract utility (part of
    MKVToolNix) which incorporates most (if
    not all) functionality of mkvextract and
    mkvinfo utilities. Written in C#NET 4.0,...
    Download gMKVExtractGUI
  • 3
    JasperReports Library
    JasperReports Library
    JasperReports Library is the
    world's most popular open source
    business intelligence and reporting
    engine. It is entirely written in Java
    and it is able to ...
    Download JasperReports Library
  • 4
    Frappe Books
    Frappe Books
    Frappe Books is a free and open source
    desktop book-keeping software that's
    simple and well-designed to be used by
    small businesses and freelancers. It'...
    Download Frappe Books
  • 5
    Numerical Python
    Numerical Python
    NEWS: NumPy 1.11.2 is the last release
    that will be made on sourceforge. Wheels
    for Windows, Mac, and Linux as well as
    archived source distributions can be fou...
    Download Numerical Python
  • 6
    CMU Sphinx
    CMU Sphinx
    CMUSphinx is a speaker-independent large
    vocabulary continuous speech recognizer
    released under BSD style license. It is
    also a collection of open source tools ...
    Download CMU Sphinx
  • More »

Linux commands

crm
crm
Use crm online using onworks.net
services. ...
Run crm
  • 4
    crmgr
    crmgr
    crmgr - administration utility for QDBM
    Curia ...
    Run crmgr
  • 5
    gappletviewer
    gappletviewer
    gappletviewer - Load and runs an applet
    ...
    Run gappletviewer
  • 6
    gaps
    gaps
    mummer - package for sequence alignment
    of multiple genomes ...
    Run gaps
  • s-processed="true">
    g15stats
    g15stats - A CPU/Memory/Swap usage
    meter for G15Daemon DESCRIPTION: The
    packages provides the following usage
    meter for LCD on some Logitech
    keyboards, usind g...
    Run g15stats
  • More »
  • Ad