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Updated EukPhylo Part 2: MSAs, trees, and contamination loop (markdown)

Godwin N. Ani 2025-04-07 15:05:22 -04:00
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EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -190,7 +190,7 @@ To run the CL, use a similar command structure as described for running EukPhylo
| --contamination_loop | yes | seq, clade | The mode in which to run the CL | none | | --contamination_loop | yes | seq, clade | The mode in which to run the CL | none |
| --nloops | no | any positive integer | Number of iterations | 5 | | --nloops | no | any positive integer | Number of iterations | 5 |
You can also change the tree-building method using the `--cl_tree_method` argument (`iqtree`, `iqtree_fast`, or `fasttree`). You can choose whether to run Guidance between each iteration, or just MAFFT, by using the `--cl_alignment_method` argument (`mafft_only` or `guidance`). Here are some mode-specific arguments: You can also change the tree-building method using the `--cl_tree_method` argument (`iqtree`, `iqtree_fast`, `fasttree` or `raxml` with the default being `iqtree_fast`). You can choose whether to run Guidance between each iteration, or just MAFFT, by using the `--cl_alignment_method` argument (`mafft_only` or `guidance` with the default being `mafft_only`). Here are some mode-specific arguments:
#### Sisters/subsisters mode #### Sisters/subsisters mode