Input species tree nodes don't match output Base_clade_results.txt nodes

[lilypeck]

Hello

Firstly thanks for making this great tool

I ran cafe5 with the below script
cafe5 -i Orthogroups.GeneCount.formatted.tsv -t SpeciesTree_rooted_node_labels_ultrametric-ape.txt

I want to annotate a tree with the cafe5 output, specifically the increase and decrease values from Base_clade_results.txt. However the nodes in Base_clade_results.txt don't match the nodes in my input species tree - how do I match these up? You can see below the nodes in my tree go upto N30, whereas in Base_clade_results.txt the nodes go much higher. I know you have the helper script which produces an annotated .png but I would rather do this myself in R.

> ultrametric_tree$node.label
 [1] "N0"  "N1"  "N2"  "N3"  "N5"  "N9"  "N10" "N6"  "N11" "N16" "N24" "N4"  "N7"  "N12"
[15] "N17" "N18" "N25" "N13" "N19" "N8"  "N14" "N20" "N21" "N26" "N28" "N29" "N30" "N15"
[29] "N22" "N23" "N27"

head results/Base_clade_results.txt 
#Taxon_ID	Increase	Decrease
<34>	1	0
GCA_013623725<1>	751	2770
WOFQ01<2>	1534	1668
<38>	242	408
<35>	0	2
GCA_013623525<3>	533	406
<52>	154	179
<36>	52	2666
<37>	64	200

Thanks

Lily

[benfulton]

It's a bit tricky, as the results in that file include all of the internal nodes in the tree as well as the tips. You can see the ID's that were assigned in the tree in the results.txt file, so you would have to match those numbers up to the species. The good news is that if you load the tree in using R's ape package, the ID's that are assigned should be the same as the ones CAFE assigns.