Do not select too few species, preferably 5 or more.
The IDs' format of the .cds sequence files of the species is best processed uniformly to avoid special characters. As my experience, it is OK to have underscores and decimal points in the numbering. It is recommended to process it uniformly as XXXX.ID.
The .pep protein sequence file of the species is translated from the .cds sequence file using the seqkit command to ensure that the IDs in .cds and .pep correspond.
The files in input_dir need to be named XXXX.cds and XXXX.pep.
The structure in phytree.nwk must be a strict binary tree, otherwise MCL in step.2 will report an error.
The species names in phytree.nwk must correspond one to one with the file names in input_dir.
Summary of Tree2gd Questions
.cdssequence files of the species is best processed uniformly to avoid special characters. As my experience, it is OK to haveunderscoresanddecimal pointsin the numbering. It is recommended to process it uniformly asXXXX.ID..pepprotein sequence file of the species is translated from the.cdssequence file using theseqkitcommand to ensure that the IDs in.cdsand.pepcorrespond.input_dirneed to be namedXXXX.cdsandXXXX.pep.phytree.nwkmust be a strict binary tree, otherwiseMCLinstep.2will report an error.phytree.nwkmust correspond one to one with the file names ininput_dir.