Param-AgalmaCapBlank.txt

# projectwd: Project working directory. Where the outfiles will be written to.
# target_aln_path: Path with target gene alignments. Must end in '.fas'. Each sequence in the alignment must match the name of the transcriptome file it came from. Leave blank if using agalma supermatrix as input. 
# target_aln_type: 'DNA' or 'AA'. Leave blank if using agalma supermatrix as input. 
# aglama_partition_file: Partition file for agalma supermatrix path. Leave blank if using DNA/AA alignments as input.
# agalma_supermatrix_file: Agalma supermatrix alignment path. Leave blank if using DNA/AA alignments as input.
# transcriptome_folder: Folder containing the transcriptome assemblies. Names must match names in supermatrix or gene alignments.
# refseqcds_path: Reference genome Refseq CDS path.
# refseqgenome_path: Reference genome path.
# refseqprotein_path: Reference genome Refseq Protein.AA path.
# supermatrix_aln_type: Type of alignment for agalma supermatrix file or gene alignments (ie 'fasta', 'phylip-relaxed'....) see https://biopython.org/wiki/AlignIO for allowed file formats.
# threads: Number of processing threads to be used in the analysis.
# min_taxoncov: Minimum number of taxa in locus for it to be included in the output.
# min_exon_length: Minimum length of exon for it to be included in the output.
# write_ref: Should the reference genome be included in the output? ['yes' or 'no']