Modifications
fasta_concatenate.pl Concatenate all contigs of a FASTA file and adds one single header name to the entire concatenated sequence
fasta_to_phy.py Transform FASTA alignment to PHYLIP alignment
keep_long_isoforms.py keep only the specified number of isoforms from a specific species proteome / ortholog group.
Re-namers
fasta_rename_nextdenovo.pl rename to simplified header post-running genome assembler NextDenovo
fasta_rename_nextpolish.pl rename to simplified header post-running genome assembly polisher NextPolish
ncbi_protfasta_renamer.pl rename to simplified header proteins downloaded from NCBI
renamer_braker_output_fasta_headers.sh simple sed rename post-braker output to add species short code for easier alignment analyses
rename_pre_phy.pl specific to a gene analysis, but modifiable to rename fasta headers pre-FASTA->PHYLIP transformation to a very short header
file_formatter_rename_space_containing_files.sh bash renamer for multiple files in a folder, where some of them contain spaces in the filename. It changes the spaces for underscores, but it can easily be modified on the script in line 16.