Frequently Asked Questions
1. How many sequences can RECUR handle?
The RECUR algorithm is fast and light weight and can be used on tens of thousands of sequences. However, if a constraint tree is not provided, RECUR is limited by the scalability of IQ-TREE.
2. Can I use IQ-TREE3?
The short answer is, yes you can!
RECUR requires IQ-TREE version 2.0 or higher to function correctly. The default IQ-TREE version bundled with RECUR is 2.4.0, which uses the binary name iqtree2. If you’re using a different version of IQ-TREE (e.g., IQ-TREE3), ensure that the corresponding binary is accessible in your environment. You can specify the binary name using the -iv or --iqtree-version flag when running RECUR. For example, to use IQ-TREE3, add -iv iqtree3 to your command.
Different versions of IQ-TREE may have variations in their command-line interfaces. To accommodate these differences, RECUR provides a config.json file that allows users to define the appropriate command structure for their specific IQ-TREE version.
If a new version of IQ-TREE (e.g., IQ-TREE4) is released, you can adapt the config.json by copying an existing configuration block (such as for iqtree2 or iqtree3) and renaming the method key to match the new binary name (iqtree4). Adjust the command parameters as needed to align with the new version’s requirements.
When running RECUR with a custom config.json, specify its path using the --config flag and indicate the IQ-TREE binary with the -iv flag:
recur [options] -f <alignment_file> --outgroups <outgroup_species/file> -st <AA|CODON> -te <treefile> --config path/to/config.json -iv iqtree4
This ensures that RECUR utilizes the correct command structure for the specified IQ-TREE version.
⚠️ Caution: While minor adjustments to the command structure can be managed via the config.json, significant changes in IQ-TREE’s interface may not be compatible with RECUR. In such cases, it’s recommended to contact the RECUR developers for guidance on updating the package accordingly.
Still have questions? Please head to our dicussion section on GitHub to check for the similiar questions and answers. If no solutions were found, please open an new issue.