Query about Expansion/Contraction number of the gene families in CAFE
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6 weeks ago
boymin2020 ▴ 30

Hi all,

Recently, I have been working on genome assembly for a teleost fish. Our protein-coding sequences from 17 teleost fishes can be clustered into 22123, of which 2226 families are single-copy orthologs. Below is one part of my pipeline: ...Orthofinder-MUSCLE-RAxML-r8s-CAFE... The Expansion/Contraction results of gene families make me confused as I am not sure the calculated numbers are right or not. My colleagues think the numbers are too big. I am writing to ask what affacts the number.

Bests,

r8s RAxML CAFE • 174 views
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Entering edit mode
6 weeks ago
M.O.L.S ▴ 40

--Expansion, -E Expansion parameter for Nelder-Mead optimizer

Evolution , birth and death rate affects the number with regards to expansion contraction results.

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