Build IQ-TREE by ourselves. This will increase build times. I tried a bit here: 0ff54925d358ed8de9d80b6ebf4eb209a272d985...120bbcfbc6c7de0c6f4fab6ebc146b45ed281a49
Use IQ-TREE version 2.3.4 which provides prebuilt binaries for both amd64 (intel) and arm64 (arm). Do this by conditionally determining the binary based on TARGETARCH similar to how csvtk is downloaded.
Context
Currently, IQ-TREE version 2.1.2 is used in the Docker image with a note that it requires emulation on non-amd64 hosts:
https://github.com/nextstrain/docker-base/blob/822a45939508929beeb3e664680f7e0d5475c549/Dockerfile#L125-L132
Possible solutions
TARGETARCH
similar to how csvtk is downloaded.