Phoenix converts EMBL flat files into some suitable XML format and then read the resulting XML files using whatever XML parser is available in your language.
Thermo MSF Parser is a Java library to parse and visualize these msf files. The Thermo ProteomeDiscoverer program is a proteomics tool that integrates both the peptide identification and quantification steps in peptide centric proteomics into a single workflow. This makes it one of the preferred programs to analyse proteomics data, coming from Thermo mass spectrometers, in a rapid and consistent manner. The results of the ProteomeDiscoverer workflow program are stored in msf files. Here,
txgen generates a script for PAUP*, to calculate MP or ML tree scores on a sliding window of nucleotide data given an input tree. The program also parses PAUP*’s log file into a table that can be used in your favourite spreadsheet.