Work with the Example Data

Identify the small inputs and recorded outputs bundled with OrthoEvolution.

The repository includes small files for ortholog searches, sequences, alignments, and trees. Use them to learn each file format or practice one operation at a time. You do not need to start with a large dataset.

These files are historical test fixtures and recorded outputs. They do not form a complete analysis or a current biological reference dataset.

Find the files

examples/example-data/
├── BLASTest_MAF.csv
├── BLASTest_TIME.csv
├── BLASTest_mygene.csv
├── HTR1A_aligned.phy
├── HTR1A_aligned_cds_nucl.fasta
├── MASTER_HTR1A_CDS1.ffn
├── example_pba.xlsx
├── organisms.csv
├── species_tree.nw
└── Alignment_Filter/
    ├── HTR1A.faa
    ├── HTR1A.ffn
    ├── HTR1A_G2.faa
    ├── HTR1A_G2.ffn
    ├── HTR1A_G2_aa.aln
    ├── HTR1A_G2_removed.ffn
    ├── HTR1A_P2N_na.aln
    ├── AA_Guidance2/
    └── NA_Guidance2/

The GUIDANCE2 directories contain intermediate scores, alignments, and filter files. Keep them with the input and final alignment. Together, these files show which sequences or columns the filter removed.

Choose an example by task

Task	Start with	What it demonstrates
Inspect accession tables	BLASTest_mygene.csv	Gene-by-organism accession layout
Review BLAST summaries	BLASTest_MAF.csv, BLASTest_TIME.csv	Recorded accession and timing outputs
Practice protein alignment	Alignment_Filter/HTR1A.faa	Multi-sequence protein FASTA input
Inspect coding sequences	Alignment_Filter/HTR1A.ffn	Matching coding-region nucleotide FASTA
Inspect a filtered alignment	Alignment_Filter/HTR1A_G2_aa.aln	Recorded GUIDANCE2-derived alignment
Inspect PAL2NAL output	Alignment_Filter/HTR1A_P2N_na.aln	Protein-guided nucleotide alignment
Read PHYLIP input	HTR1A_aligned.phy	Alignment in PHYLIP format
Read a tree	species_tree.nw	Newick-formatted tree
Inspect the organism set	organisms.csv	One organism name per row

You can find these files in the repository’s examples/example-data directory.

Inspect a sequence file

from pathlib import Path

from Bio import SeqIO

sequence_file = Path("examples/example-data/Alignment_Filter/HTR1A.faa")
records = list(SeqIO.parse(sequence_file, "fasta"))

assert records
assert all(record.seq for record in records)

This test makes sure that Biopython can read at least one non-empty FASTA record. It does not test orthology, sequence quality, taxonomic coverage, or the relationship between the protein and nucleotide files.

Use the examples as snapshots

Before a tool changes an example, copy the file to a disposable work directory. Record the example name and the program version for each new result. The bundled accession values, alignment filters, and trees are snapshots. Do not treat them as current data.