Upgrade IQ-TREE to 2.3.5 with CMAPLE support #228
Conversation
We want the CMAPLE support (first available with 2.3.4) for better and faster trees. CMAPLE support is optional and not all release builds of IQ-TREE have it enabled. So far, it seems that the "main" releases are made without CMAPLE support (e.g. 2.3.5) and then parallel releases are made with it (e.g. 2.3.5.cmaple), but only for x86_64 on Linux and macOS. Thus, we're still not using an aarch64/arm64 binary even though the "main" releases (without CMAPLE support) provide them. If we keep waiting, maybe they'll start being provided, or, eventually, we can start compiling them ourselves. That's for another time, though. Resolves: <#226>
|
This upgrades IQ-TREE from 2.1.2 to 2.3.5.cmaple. I scanned the release notes between those versions and didn't notice any major breaking changes. |
There was a problem hiding this comment.
12 ✅ for the pathogen-repo-ci jobs 🎉
Slightly tangential, does this warrant updating the citation in augur tree?
|
Uh… maybe! Augur's not guaranteed to use an IQ-TREE with CMAPLE support, but it does us no harm to update the citation. |
\o/ That said, my understanding here is that we'd not necessarily expect these to fail with CMAPLE support but get faster and/or better trees. And our pathogen CI isn't checking tree quality—that's still the sole domain of 👀 unfortunately—so potentially we've accidentally made the trees worse in some way with this change and wouldn't know via automated checks. But that would be contrary to expectations. |
|
Thanks, @tsibley! I'm sure @bqminh will be happy to see this. He has previous said they would try to prioritize CMAPLE + ARM support.
We'd have to opt into the CMAPLE algorithm in our tree rules with the tree builder arg |
|
Yes, @trongnhanuit and me are happy to see it happening ;-) thanks! |
We want the CMAPLE support (first available with 2.3.4) for better and faster trees.
CMAPLE support is optional and not all release builds of IQ-TREE have it enabled. So far, it seems that the "main" releases are made without CMAPLE support (e.g. 2.3.5) and then parallel releases are made with it (e.g. 2.3.5.cmaple), but only for x86_64 on Linux and macOS. Thus, we're still not using an aarch64/arm64 binary even though the "main" releases (without CMAPLE support) provide them. If we keep waiting, maybe they'll start being provided, or, eventually, we can start compiling them ourselves. That's for another time, though.
Resolves: #226
Checklist