Q:

Recently, I have read your
published paper named" PseudoPipe: an automated pseudogene identification
pipeline"( Vol. 22 no. 12 2006, pages
1437–1439/doi:10.1093/bioinformatics/btl116), which impressed me so much. I
really admire your and co-workers’ excellent work.
After reading the literature, I downloaded the PseudoPipe program(Pipeline
Source Code) at http://pseudogene.org/ and tried to use it to identify
pseudogene sequences in mammalian genome.But there are some questions
during pre-experiment.I input the exsiting data
(caenorhabditis_elegans_62_220a) and installed Python 2.26，howeverthe
PseudoPipe program failed to run the parseFastaAlignment.py.I analysed the
fastaAlign did not do well.It really puzzle me a lot, and I will appreciate
it if you can solve them for me.

A:
Please note that PseudoPipe was written to discover pseudogenes in mammalian genomes, it does not work well in C. elegans.