how i can extract the orthologous sequences
Hi, I used proteinortho on 15 proteomes to extract the orthologue sequences a. I got a matrix prteinortho.txt. could you tell me how i can extract the orthologous sequences between the 15 species to build a phylogeny. Thank you in advance for your help.
# Species Genes Alg.-Conn. Sample1.fasta Sample2.fasta Sample3.fasta Sample4.fasta Sample 5.fasta Sample6.fasta Sample7.fasta Sample8.fasta Sample9.fasta...... Sample 15
15 15 1 FKA_08408-RA ZKA_09992-RA FKC_10499-RA FG005_03202-RA FKN_11022-RA FKR_00001-RA FG851_09649-RA FKL_12190-RA FKT_08425-RA
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Something is missing.
I forgot to cut the first column of matrix.
How do you define 'orthologous' ? only 1-to-1 ? also 1-to-many? many-to-many?
according to the manual: the matrix is based on the algebraic connectivity of the respective group. A connectivity of 1 indicates a perfect dense group with each gene similar to each other gene.
Hi h.mon I saw this note in the manual but I did not find an example of use for grap_proteins.pl (is it necessary for example that I give the matrix with the 15 proteomes???,)
Please use the
ADD COMMENTbutton when commenting on someones answer.Did you try to run the script without arguments? It should output some help:
You can also use orthofinder.py tool to get ortholog proteins in your data set. And you will be able to see how many single copy (one-to-one) orthologs are in your dataset. In phylogenetic analyses based on ortholog proteins mostly single copy orthlolog proteins are used.
I will try to use it and come back to you. thank you