Treemix - collapsed branches
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Ollie White
Jan 30, 2017, 10:59:02 AM1/30/17
to structure-software
Hello,
I am trying run Treemix on some RAD data from a group of non-model plant species, to build a ML tree while inferring migration events.
The software seems to be running OK but the output seems odd... the tree is collapsed and doesn't seem able to resolve the evolutionary relationships, especially compared to a RAxML tree that we have already processed based on the same data.
The manual mentions turning off sample size correction using the noss flag and that does help somewhat but the tree is still very much collapsed with small branch lengths.
The input data is based on 5332 SNPs and I am using a treemix file that was output by stacks.
Just wondering if anyone has experienced something similar or has advice about things to try.
Kind regards
Ollie
I am trying run Treemix on some RAD data from a group of non-model plant species, to build a ML tree while inferring migration events.
The software seems to be running OK but the output seems odd... the tree is collapsed and doesn't seem able to resolve the evolutionary relationships, especially compared to a RAxML tree that we have already processed based on the same data.
The manual mentions turning off sample size correction using the noss flag and that does help somewhat but the tree is still very much collapsed with small branch lengths.
The input data is based on 5332 SNPs and I am using a treemix file that was output by stacks.
Just wondering if anyone has experienced something similar or has advice about things to try.
Kind regards
Ollie
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