In your current workflow, the sequence IDs in the FASTA headers, such as "AT3G02650.1|PACid_19663616" and "evm_27.model.AmTr_v1.0_scaffold00066.198", will serve as the taxon names in the resulting species tree. IQ-TREE treats these headers as the labels for the leaves in the phylogenetic tree. This means the tree branches will be labeled with these sequence IDs instead of readable species names like "Arabidopsis" or "Amborella".

You are missing a step to achieve readable species names. Before concatenation, replace the sequence IDs in each aligned FASTA file with the corresponding species name. Since these are single-copy orthologs from OrthoFinder, each file contains one sequence per species. Use a script to map and rename the headers. For example, create a mapping file (e.g., species_map.txt) with lines like:

AT3G02650.1|PACid_19663616  Arabidopsis
evm_27.model.AmTr_v1.0_scaffold00066.198    Amborella

Then, use a tool like sed or a Python script to rename headers in all *_trim.fa files. Here is an example Python script:

import sys
from Bio import SeqIO

mapping = {}
with open('species_map.txt') as f:
    for line in f:
        seq_id, species = line.strip().split('\t')
        mapping[seq_id] = species

for record in SeqIO.parse(sys.argv[1], 'fasta'):
    if record.id in mapping:
        record.id = mapping[record.id]
        record.description = ''
    print(record.format('fasta'))

Run it as:

python rename_headers.py input_trim.fa > output_renamed.fa

Repeat for all files, then concatenate.

Your proposed IQ-TREE command is suitable for a first species tree, as it uses ModelFinder Plus (-m MFP) for automatic model selection, ultrafast bootstraps (-bb 1000), and SH-aLRT branch tests (-alrt 1000). However, for better accuracy with a concatenated supermatrix, use partitions to allow different evolutionary models per orthogroup. Modify your command to:

iqtree -s supermatrix.phy -p partitions.txt -m MFP -bb 1000 -alrt 1000

Use -spp instead of -p if you want partition-specific branch lengths, but this increases computation time. Ensure your partitions.txt is in the correct format for IQ-TREE (e.g., without "PROT," if specifying models manually, but MFP handles it).

Kevin