Masel Lab documentation changes#26
Open
phylowheeler wants to merge 30 commits into
Open
Conversation
Recommending +R instead of +G on the quickstart page
Added tip about use of QC models. Added citations for QC models
Recommended more strongly using +R instead of +G, citing (Ferretti et al., 2026). Removed the tip regarding the outdated +TEST option vs the more up to date +MFP option, which includes the free rate model
added example run for protein sequence using a sample amino acid alignment and QC.pfam model
Added a paragraph to the section on alignment filtering to suggest Prequal (prior to alignment), Divvier, Taper, and CLOAK as good options for filtering protein alignments
clarified edits to alignment cleaning and removed references to trimal and gblocks
Expanded the description of how CLOAK works and when it should be used
Added a section on how to filter alignments prior to substitution model training to generate QC matrices
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This fork contains all our proposed changes the IQTree documentation. Mostly these center around adding information about cleaned QC substitution models, and shifting recommendations towards using +R rather than +G for rate heterogeneity among sites, in light of Ferretti et al. 2026.