Simple script to convert phylip files into FASTA files.
Can be installed adding to the profile source the following string:
alias phylip2fasta=python /{path_to}/phylip2fasta/phylip2fasta.py
If you can't don't worry, you can just launch it with python /{path_to}/phylip2fasta/phylip2fasta.py every time.
phylip2fasta -i {input}.phy -o {output_name}
-i / --input-phylip : specify the phylip (.phy) file to convert to FASTA;
-o / --output-name : specify the output FASTA file name; .fasta will be automatically added at the end of the output file.
A nice employment of this script is piping it to edgardomortiz's vcf2phylip to rapidly convert VCF files into FASTA files.
Another nice script to directly convert VCFs into FASTAs is raveancic's fromhaplomulti-VCF2FASTA.
A script to reverse convert FASTA files to phylip files is distributed with the latest version of RAxML.