Hi Mensur, sorry for this but I'm a little stuck.

I’m trying to build a species tree for the first time and I would like to clarify a few doubts regarding sequence labels and the workflow I’m following.

Data In my Single_Copy_Orthologue_Sequences folder I have files like:

ls
N0.HOG0000162.fa
N0.HOG0000271.fa

Example content of N0.HOG0000162.fa:

>AT3G02650.1|PACid_19663616
MLRSFLCRSQNASRNLAVTRISKKKTQTTHSLTSLSRFSYLESSGNASVRNIRFFSTSPPTEENPVSLPADEIPISSAAE...
>evm_27.model.AmTr_v1.0_scaffold00066.198
MWRYSLLRASSIRSQWLNRANPKTLASTSALSSCLEVYTNHRKNHGNPSFMSRESHSVAETSSYDGGNPSFSSNVSDGSS...

The first header corresponds to Arabidopsis The second header corresponds to Amborella

My workflow was:

Step 1: Orthofinder
orthofinder -f ./prot_longest -t 30 -o orthofinder


Step 2: mafft 
mafft --auto --thread 30 "$file" > "$output_file"


Step 3: trimal
trimal -in "$file" -out "$output_file" -automated1- -fasta -htmlout "$output_file"


Step 3: Concat
Concat: https://github.com/nylander/catfasta2phyml
$CATFASTA --concatenate ${ALIGN_DIR}/*_trim.fa > $SUPERMATRIX 2> $PARTITIONS

# Clean file names and prepare partitions for IQ-TREE/RAxML (protein)
sed -i -e "s#${ALIGN_DIR}/##" -e "s/_trim.fa//" -e "s/^/PROT, /" $PARTITIONS

Example output of supermatrix: head supermatrix.phy

10 893113
AT3G02650.1|PACid_19663616    MLRSFLCRSQNASRNL...
evm_27.model.AmTr_v1.0_scaffold00066.198  MWRYSLLRASSIR...

Partition file (partitions.txt):

PROT, N0.HOG0000162 = 1-560
PROT, N0.HOG0000271 = 561-1440
PROT, N0.HOG0000277 = 1441-2422

Questions:

I notice that I don’t have clear species labels in my headers, only sequence IDs.

In the resulting species tree, how will my species be labeled?

Will IQ-TREE use these IDs as taxon names?

Am I missing a step if I want readable species names (like “Amborella”) in the final tree?

I was thinking of running IQ-TREE like this:

iqtree -s supermatrix.phy -m MFP -bb 1000 -alrt 1000

Is this correct for a first species tree?

Should I consider using partitions (-spp partitions.txt) here?

Thank you very much for your help!