Hi there, this is a personal repository containing some scripts I used in my bioinformatic research. All the solutions are quick-and-dirty, easily to use. If you want some more functions, email me nevrfa#gmail
Current scripts:
FormatConvert
- fasta2nexus.pl: A quick-and-dirty script to convert Fasta files to Nexus files.
- nex2nwk.pl: Simple script to convert nexus trees into newick trees. BioPerl is required.
- extract_fasta_from_beast_xml.pl: Extract fasta files from multi-sample BEAST xml file.
SequenceManipulate
- changetags.pl: Simple script to change fasta tags with given new tags.
- fasnochangeline.pl: Convert 80/100-bp-per-line fasta file into no change line fasta file.
- lengthfilter.pl: This script filters sequence shorter than given length.
- merge_sequences.pl: combine multiple fasta file into one (only merge sequences with same tags and in the same order).
- pick_subalignment.pl: Pick out subalignment from a huge alignment file.
- remove_common_gap.pl: Remove common gaps in multi-alignment. You can define a cut ratio.
Enjoy!