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In `axml.h`, the `rawdata->sites` variable is defined as type `int`. Attempting to compress an alignment with about 3B positions is resulting in a "too few sites" error, presumably because we are over…
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For the 2000 taxon dataset it seems that for some models we are not getting the correct log-likelihood. Specifically:
### DAYHOFF
| Program | log-likelihood |
| --- | --- |
| **phyml** | -588223.2856…
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If the shape of the Gamma distribution is low enough, it might happen that the likelihood scores of different categories require different scaling. That means that at some point it is very likely that…
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I was just wondering if there is a reason that RAxML does not write its error messages to _stderr_ rather than to _stdout_. I want to run it from programs and scripts where capturing error output sep…
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Hi,
I've worked with v8.1.20 for the past year with good success but recently decided to upgrade to the newest version (v8.2.4) after doing some spring cleaning. I was able to use the 8.2.4 to do so…
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Currently, pattern compression is implemented on a "character level", i.e. it works with the strings as they were read from a FASTA/PHYLIP file. This has at least one unpleasant side effect: if severa…
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Fix the persite log-likelihood functions to account for tip patterns and also the new way of handling mixture models.
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Offer core LLPLL functions that do not require passing a partition data type as argument, but just C arrays and variables, this will facilitate integration with ExaML.
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A CLV update function, that only updates between indices i and j, where 0