Adding species but not repeating the mapping of existing species

[Yuqia]

Hello,

I'd like to add more species to the previously built tree. Is there a way to re-use the mapping information of the previously included species and add this information to the mapping information of the newly added species, instead of re-mapping all previously included species again?

Thank you.

[mudymudy]

I guess you could just back up your concatenated MSA (.phy) and the tree files in a different folder. Then just run:

read2tree --standalone_path marker_genes/ --output_path output --reads species3_R1.fastq species3_R2.fastq

An n' number of times depending on how many samples you want to add, then finally:

read2tree --standalone_path marker_genes/ --output_path output --merge_all_mappings --tree

You will basically create a new concatenated alignment with the newly incorporated samples with the new tree inference at the end. Hope it helps.