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When i ran GERP like " ./gerpcol -t ./test/align/NeuTree.txt -f ./test/align/29Mamms_Alignment.mfa -e human" , it reported like " Tree species ajbat not present in alignment and therefore ignored.
Tree species armadillo not present in alignment and therefore ignored.
Tree species baboon not present in alignment and therefore ignored.
Tree species cat not present in alignment and therefore ignored.
Tree species chimp not present in alignment and therefore ignored.
Tree species cow not present in alignment and therefore ignored.
Tree species dog not present in alignment and therefore ignored.
Tree species dusky_titi not present in alignment and therefore ignored.
Tree species galago not present in alignment and therefore ignored.
Tree species gorilla not present in alignment and therefore ignored.
Tree species hedgehog not present in alignment and therefore ignored.
Tree species horse not present in alignment and therefore ignored.
Tree species human not present in alignment and therefore ignored.
Tree species lemur not present in alignment and therefore ignored.
Tree species macaque not present in alignment and therefore ignored.
Tree species marmoset not present in alignment and therefore ignored.
Tree species mouse not present in alignment and therefore ignored.
Tree species mouse_lemur not present in alignment and therefore ignored.
Tree species muntjak_indian not present in alignment and therefore ignored.
Tree species nrooted
(((opossum:0.034160,monodelphis:0.022496):0.032669,wallaby:0.049042) not present in alignment and therefore ignored."

but my Alignment.mfa had these species,. Can you give me a solution, thank you in advance.

Hi! I am trying to run GERP++, but I am running onto a wall, because the page that should host the software is unavailable, and the Sidow Lab is not answering to emails.
I was wondering if the tarball in this repository could be used to run GERP++, and if you had a user manual somewhere, or a workaround to find information about the program that are not on the paper.

Thank you!

Heys,
Could you please upload the test dataset that they share?
http://mendel.stanford.edu/SidowLab/downloads/gerp/GERP_test_data_200802011.tar.gz
My computer is not able to access it.

Thank you!

When I used the data to test, there was an error, such as the following:

I don't know what went wrong, how did you deal with it at that time, could you tell me, thank you in advance

Hi，
I've got multiple alignments using LAST. According to the README, the GERP score output file should contain each position of the alignments. But I found that the lines of RS score file far exceed the aligned sites. How should I comprehend the result?
Thank you very much!