orthohmm_filter_tree

Process the results output by orthohmm software.

Filter orthogroups and then infer the phylogenetic tree.

Simple analysis process, configure the required environment by yourself.

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step1_prepare.sh

• Get less variation in the number of homologous genes and more species with homologous genes.
• Mainly use deal_orthohmm_gene_count.py script to calculate orthohmm_gene_count.txt and then extract cds sequence.

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step2_make_all_command.sh

• Make all command to get best unique homologous gene.
• Improve cds sequences whose length is not a multiple of three.
• Of course you can choose not to filter.

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step3_OMM_MACSE.sh

• OMM_MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

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step4_FastTree.sh

• Constructing gene trees.

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Finally, inferring species trees from gene trees by astral-pro3 or tree-qmc.

Of course, you can use 4d site sequences for analysis, or connect all multiple sequence alignment files into supergene for analysis (merge_phy.py).

example:

tree out/OG06164
|-- OG06164.best
|-- OG06164.best.fa
|-- OG06164_best_sequences.fasta
|-- OG06164_config_backup.conf
|-- OG06164_file_manifest.txt
|-- OG06164_pipeline_report.txt
|-- OG06164_processing.log
|-- OG06164_quality_best_sequences.fasta
|-- OG06164_quality_removed_sequences.fasta
|-- OG06164_removed_sequences.fasta
`-- omm_macse
    |-- OG06164_final_align_AA.aln
    |-- OG06164_final_align_AA.aln.phy
    |-- OG06164_final_align_NT.aln
    |-- OG06164_final_align_NT.aln.phy
    |-- OG06164_final_align_NT.aln.phy.gaps.4d.phy
    |-- OG06164_final_align_NT.aln.phy.nogaps.4d
    |-- OG06164_final_align_NT.aln.phy.nogaps.4d.phy
    |-- OG06164_final_mask_align_AA.aln
    |-- OG06164_final_mask_align_NT.aln
    |-- OG06164_final_unmask_align_AA.aln
    |-- OG06164_final_unmask_align_NT.aln
    |-- OG06164_final_unmask_align_NT.aln.phy.nogaps.4d
    |-- OG06164_maskFull_detail.fasta
    |-- OG06164_maskFull_stat.csv
    |-- OG06164_maskHomolog_stat.csv
    |-- all.phy.gz
    |-- all.tree.gz
    |-- all.tree.nwk
    `-- readme_output.txt