Authors Don Gilbert software@bio.indiana.edu

Please cite If you use this tool, please cite Don Gilbert software@bio.indiana.edu

Galaxy integration Andres Gwendoline, Institut Français de Bioinformatique.

Support For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr

Readseq

Description

Compute a phylip tree from a fasta alignment.

Workflow position

Upstream tools

Name	output file(s)	format

Downstream tools

Name	output file(s)	format
fastme	Newick tree	Newick
Rooting	out tree	Newick

Input file

Fasta file: The input data file contains sequence alignment(s)

Parameters

Output name: Output base name for the ouput files

Output files

Output_name: Resulting tree in phylip format
Output_name.log: Log file

Dependencies

ReadSeq: readseq.jar at 10.03.13 version

Working example

Input files

Fasta file

>IRAT112 GAGAACCGTCCTGTAAGTACTCTTGCTTTAAGTAATAAAGTAATACTAATCCATGACGCTTAAGTCGAAGAGAGAATAAGTCAATATTTAATTGGACTCATCGCTTATTATCATTATGAATCAATAAACAACTTGATGTTGTGCTCCATGTACGATATATAAAGACAGATA
>KARASUKARASURANKASU GAGAACCGTCCTGTAAGTACTCTTGCTTTAAATACGAAAGTAATACTAATCCATGACGCTTAAGTCGAAGAGAGAATAAGTCAATATTTAATTGGACTCATCGCTTATGTTCATCATGAATCTATAGTTAACTTGATGTTGTGCTCCATGTACGATATAAAAAGTTAGATA

Parameters

Output name -> phylip conversion

Output files

phylip conversion

168 5125
IRAT112      GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT
KARASUKARA   GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT