Sequence analysis scripts used in Wolf/Takebayashi lab

This page documents how to use perl scripts written by Naoki Takebayashi. The documentation is not complete yet, and it will be gradually added. Currently, these scripts are installed for UAF users in /usr/local/bin of catfish (teaching linux server) or /scratch/compbio/bin of tuxedo (LSI login server). These scripts are all released under GPL, so feel free to use and modify them. If you notice problems, please let me know. For beginners: Files are downloadable by copying each script into a text file ending in ".pl". You must have Perl installed on your computer unless you are using a server. For information on using Perl: Naoki's introduction to perl, Learn Perl, Learning Perl.

FASTA file manipulation tools

Simple analysis from FASTA files

File format conversion: convert FASTA/phylip file to other formats

All of these scripts have the similar usage, and it takes a input file name as the argument.
Example, convert fasta to paml format seq.fasta > seq.paml 

Other scripts, which will be documented in the future

Phred/Phrap/Consed related scripts

All scripts in alphabetical order