I would appreciate if all supporting arches (x86, ppc) would stabilise sci-biology/t-coffee. It has been in Portage for a while and works well. Sources for the latest current stable version are no longer available, so I want to remove that version ASAP. Test instructions: After compiling t-coffee, copy the "sample_seq1.fasta" file from "/usr/share/t-coffee/example" to your home directory. This file contains the amino acid sequences for four homologs of a protein in different species. Run "t_coffee sample_seq1.fasta" to have t-coffee align the sequences, calculate the alignment scores, construct a dendrogram, etc. Output files are created in the working directory. You can check the validity of the calculations by comparing the file "sample_seq1.aln" with the file I am attaching. (This output file is also available in the example directory, but it was created with an old version of the program, and the formatting is a bit different so you would have to compare the files manually. With the provided file, a diff should suffice.) The only difference between the files should be the CPU time used for the calculations. Thanks in advance,
Created attachment 119904 [details] Reference sequence alignment
x86 stable
I'm seeing some differences between the output of t-coffee and your file: diff sample_seq1.aln sample_seq1.aln.bugzie 1c1 < CLUSTAL FORMAT for T-COFFEE Version_4.96 [http://www.tcoffee.org], CPU=0.17 sec, SCORE=34, Nseq=4, Len=81 --- > CLUSTAL FORMAT for T-COFFEE Version_5.05 [http://www.tcoffee.org], CPU=0.08 sec, SCORE=33, Nseq=4, Len=81 2a3,4 > hmgl_trybr kkdsnapkramtsfmffssdfrskhsdls-----ivemskaagaawkelgpeerkvyeem > hmgt_mouse -----kpkrprsayniyvsesfqeakdds-----aqgklklvneawknlspeekqayiql 4d5 < hmgl_trybr kkdsnapkramtsfmffssdfrskhs-----dlsivemskaagaawkelgpeerkvyeem 6,7c7 < hmgt_mouse -----kpkrprsayniyvsesfqeakddsaqgkl-----klvneawknlspeekqayiql < ***. ::: .: .. .. . * . *: * : : --- > ***. ::: .: .. .. . . * . *: * : : 9d8 < hmgb_chite aatakqnyiralqeyern-gg 11d9 < hmgl_wheat anklkgeynkaiaaynkgesa 12a11,12 > hmgb_chite aatakqnyiralqeyern-gg > hmgl_wheat anklkgeynkaiaaynkgesa
beer >> coffee; sending back to maintainer... :P
confirmed on an another G4. ribosome?
This should not happen, so I think it is best for version 4.96 not to be stabilised on PPC. These variations could be caused by the magnification of a small number-rounding difference. The differences are very small, though, and probably do not impact the alignment's validity, so I do not think it is necessary to mask t-coffee in the PPC profiles. This leaves the problem of missing sources for the last (and only) stable PPC version. I suggest dropping the stable keyword and having t-coffee available only in the testing branch (for PPC). What do you PPC folk think?
(In reply to comment #6) > This leaves the problem of missing sources for the last (and only) stable PPC > version. I suggest dropping the stable keyword and having t-coffee available > only in the testing branch (for PPC). > > What do you PPC folk think? That's okay for us. Just drop the stable-version and keep the current version ~ppc. So, let's close this bug.
