-a flag seeming to not work

[Rob-murphys]

I have around 122 (so 122 orthologs) from 34 different genomes and I am trying to use the -a flag to collapse the gene trees into a phylogenetic tree with 34 nodes but it is not working. I just get a tree with the number of nodes == number of gene trees

I believe I am formatting the input file for -a correctly:

#Format
species_name: gene1,gene2,gene3,gene4,gene5
#Example
RB17:bacteria_RB17_1874945at2,bacteria_RB17_1830156at2,bacteria_RB17_1940575at2,bacteria_RB17_932854at2,bacteria_RB17_1701531at2,bacteria_RB17_1842956at2,bacteria_RB17_1676462at2

Where RB17 is the species name and the gene name in a node name for the gene tree 1874945at2 being bacteria_RB17_1874945at2.

So I have a gene tree for 1874945at2 with 34 nodes where each node if formatted as bacteria_[sample_name]_[gene_name] and so on like this for.

Is a potential reason because Astral PRO is reading in 2136 trees from my multi tree nwk file? it does however say the correct number of input trees?

The number of input tree read is 122
2138 trees read from /home/lamma/faststorage/actinobacteria/busco/busco_nt/raxml-ng-output/gene_trees.nwk
122 extra trees.
All output trees will be *arbitrarily* rooted at bacteria_RB1_1009041at2

I am happy to share the whole gene list file and gene trees.nwk file if you would like :)

[chaoszhang]

Hi Lamm-a, Sorry for the confusion, can you use the following format instead?

bacteria_RB17_1874945at2 RB17
bacteria_RB17_1830156at2 RB17
bacteria_RB17_1940575at2 RB17

Best regards, Chao Zhang

[Rob-murphys]

Hi Chao,

so for each gene a new line of

gene_name species_name

I will try this, thanks :)

[smirarab]

Chao, would be good to update to support both formats. Similar to #3