Home - Sun-Yanbo/FasParser GitHub Wiki

Welcome to the FasParser wiki!

To achieve an objective of simplifying many common tasks in sequence manipulation for biologists, I provide a new software package named ‘FasParser’. It is designed with a user-friendly GUI and a batch processing mode, which allows users to handle multiple sequence files in a simple way. Presently (v2.0+; download the latest version here, the main functions of FasParser involve:

  1. batch performing alignment construction with Muscle (Edgar, 2004), Mafft (Katoh, et al., 2002), or Prank (Loytynoja and Goldman, 2005);
  2. alignment trimming on poorly-aligned regions;
  3. alignment format conversion between FASTA and either PHYLIP, PAML, or NEXUS;
  4. sorting & renaming sequences according to accession numbers or sequence length;
  5. concatenating & merging sequences for a particular set of samples from multiple sequence files;
  6. (back-)translation and ORF prediction;
  7. extracting and filtering sequences according to ID, sequence length, or sequence similarity;
  8. detecting positive selection with CodeML (Yang, 2007);
  9. designing PCR primers with Primer3 (Rozen and Skaletsky, 2000), and
  10. extracting consensus-aligned regions between different aligner results (for a same gene). Moreover, there has been designed a specialized Editor for FasParser (v2.0+) to easily viewing and editing sequences.

Below is the homepage view of FasParser2: Homepage of FasParser2