Author: Léo-Paul Dagallier
Last update: 2024-02-06
In the concatenation approach we will first concatenate the MSAs of all the loci into a single MSA (or ‘supermatrix’), and then infer the species tree from the supermatrix.
Here we’ll present species tree inference with RAxML and IQ-TREE. With RAxML, the MSAs for all the loci need to be concatenated into a single supermatrix prior to RAxML inference. With IQ-TREE, we can directly input all the MSAs files that will be concatenated internally by IQ-TREE.
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Under construction, more coming soon. (feel free to send me an email or open an issue to pressure me)
Draft:
To concatenate matrices: https://github.com/marekborowiec/AMAS/