#20

Help on getting multiple alignment for PhyloCSF

Hello Dr. Lin, Thanks a lot for the contribution of PhyloCSF. I'm trying to use PhyloCSF to evaluate the likelihood that some novo ORFs were protein coding. These ORFs were found by performing ORF-RATER ...

#19

[ERROR] No package named ocaml+twt found.

Hi, I'm trying to install PhyloCSF on CentOs 7. When I run : opam install batteries ocaml+twt gsl I get the error: [ERROR] No package named ocaml+twt found. gsl and batteries installed. How can ...

  • Opened by shlomita Jan 31, 2017
  • 1 comment
#18

PhyloCSF fails with GSL_exn exception

Run PhyloCSF with parameters "100vertebrates" and the attached 2-codon fasta alignment. chr19-44274475-44274480-.hg38_100.txt It fails with this message: exception 0 5 Error.Gsl_exn(_) failure ...

#17

rm: cannot remove './PhyloCSF/src/_build': Directory not empty

I got an mistake after running make . Can anyone help me? I would appreciate it very much. ocamlfind install CamlPaml META _build/CamlPaml.cmi _build/CamlPaml.cma _build/CamlPaml.cmxa _build/CamlPaml.a ...

#16

ocaml+twt not found

opam install ocaml+twt [ERROR] No package named ocaml+twt found. opam --version 2.0~alpha5 when i use version 1.2.2, it still tell No package named ocaml+twt found.

  • Opened by cha1n Oct 21, 2016
  • 3 comments
#15

Issue with completing run

Mike Lin, I have recently downloaded and successfully installed PhyloCSF on Mac OS X Mavericks, however I am having an issue running the program with FASTA alignments I have generated, which I will describe ...

#13

Unbound module Gsl

Dear Mike Lin: I follow the "Obtaining the PhyloCSF software" step on the wiki page,but when I execute make command under PhyloCSF folder,Errors occur: zhangjun@ubuntu:/usr/local/src/PhyloCSF$ ...

#12

Fatal error on running PhyloCSF in too old kernel system

Dear Mike Lin, I met a problem when I run PhyloCSF in our linux system. It reported that 'FATAL: kernel too old'. Could you help me how to solve this problem. Many thanks, Jie

  • Opened by msswjw Dec 11, 2012
  • 2 comments
#11

I use ocaml 4.00.1 and there are some syntax errors in file /lib/CamlPaml/Expr.ml

line 67-90: | Add (l,r) -> Buffer.add_char b '('; f l; Buffer.add_string b " + "; ...