how to determine the exact amino acid with different effect strength

vlanore / diffsel

A C++ program to detect convergent evolution using Bayesian phylogenetic codon models.

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how to determine the exact amino acid with different effect strength #4

Closed kanglizhu closed 5 years ago

kanglizhu commented 5 years ago

Hello, After running readdiffsel, i checked the *.signdiffsel file. This file contains four colums: site number, aminoacid number, "convergence probability", and effect strength.

Site number ranges from 0 to (total_base_numbers/3 -1 ), and "site number + 1" is the position in the sequence alignment.

From a series of "*.signdiffsel files", i find the amino acid number ranges from 0 to 19. Now if i want to know the exact amino acid for one animo acid number, can you please explain what should i do next?

Best wishes, kangli

vlanore commented 5 years ago

Hello,

Aminoacids are ordered this way in diffsel: {'a', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm','n', 'p', 'q', 'r', 's', 't', 'v', 'w', 'y', '-'}; So for example aminoacid 4 would be f, 19 would be y.

Sorry this wasn't explained in the README. I hope this answers your question.

kanglizhu commented 5 years ago

Hello，

Thank you so much for your help. Now i know clearly how to get the exact amino acids.

Best wishes, kangli