GERP++

The code from GERP++ Home Page is not available, but I found a copy in Github tvkent/GERPplusplus. You can also find it here.

After downloading it, unzip it and run make. (Please note that only available in Linux, can't in Windows)

How to run?

-t tree file -f fasta file -e target -a fasta format -v see logs

./gerpcol -t NP_000006.2.blast.dnd -f NP_000006.2.blast.aln.fa -e NP_000006.2 -v -j -a

I found the code from github can't run.

Correct the code from github, and run successfully. But it only can calculate scores for ATCG.

Error Source

When reading MSA in fasta sequences, it will read one more special char (maybe \n), which makes it can't map the MSA to tree file.
How to solve?
1. Update 71th line in gerp__KRT from return _title; to return _title.substr(0, _title.length() - 1);
2. Run make
3. Use it!!
Example
1. The origin code from github gerp++KRT
2. The modified code gerp++KRT_patch
  - gerpcol executor gerpcol
  - MSA Fasta input NP_000006.2.blast.aln.fa
  - Tree input NP_000006.2.blast.dnd
  - Result NP_000006.2.blast.aln.fa.rates
  - Command ./gerpcol -t NP_000006.2.blast.dnd -f NP_000006.2.blast.aln.fa -e NP_000006.2 -v -j -a
Note

My input examples come from ClustalOmega, and fasta file is generate by biopython.
Make tree file in one line without space string.
It will only calculate the results for ATCG, can't apply to protein seq.

XDcat/GerpHelper