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bredelings / BAli-Phy

Bayesian co-estimation of phylogenies and multiple alignments via MCMC
http://www.bali-phy.org/
GNU General Public License v2.0
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A set of edits to the manual file (README.itex.xml) #14

Closed karolisr closed 3 years ago

karolisr commented 3 years ago

The PR fixes misspellings, incorrect reference links, and other tiny edits in the manual. Also, it standardizes the reference format. I tried to make very small commits with descriptive messages.

~Take a closer look at the b9396cbb182c6b3b8ecc241256e36ef9e1ed50d2, there is an inconsistency in the way the substitution model (gtr) for fMutSel0 is described in the manual and what substitution model (hky85) BAli-Phy actually uses when using the fMutSel0 model.~

I just saw this was addressed in 74b8779acf9dffffd24311035b14d035cdfb0bbc. Disregard b9396cbb182c6b3b8ecc241256e36ef9e1ed50d2.

bredelings commented 3 years ago

Thanks for catching these! I think the changes are good to go, now that the fMutSel0 model issue is fixed.

I also want to change some of the paper links to the form that starts with https://doi.org, since that will redirect to the correct destination even if the journal moves the article URL. Would you be interested in doing that in this PR? Otherwise I will do it after I merge the PR.

karolisr commented 3 years ago

No problem, I will take care of the links (convert them to the DOI form) tonight.

bredelings commented 3 years ago

That's great - thank you!