calculate_alignment_stats: Calculate summary statistics for an alignment.
In joelnitta/baitfindR: Find Baits for Sequence Capture

Description Usage Arguments Value

Including the original alignment in the output with include_aln can be useful for mapping calculate_alignment_stats over a list of alignments with map_df to sort and filter alignments by their summary statistics.

calculate_alignment_stats(
  alignment,
  cutoff = 120,
  cutoff_any = FALSE,
  include_aln = FALSE
)

`alignment`	Input alignment; must be a matrix of class "DNAbin".
`cutoff`	Numeric value indicating minimum exon length (optional); flag this alignment if any/all exons are less than the cutoff length.
`cutoff_any`	Logical; Should the alignment be flagged if any exons are shorter than the cutoff? The default, FALSE, means that the alignment will only be flagged if all exons are shorter than the cutoff value.
`include_aln`	Logical; Should the original alignment be included in the output list?

A list including the following summary statistics:

intron_lengths: List including vector of intron lengths
exon_lengths: List including vector of exon lengths
num_introns: Number of introns
num_exons: Number of introns
mean_dist: Mean genetic distance between sequences in alignment
max_dist: Maximum genetic distance between sequences in alignment
GC_content: Total %GC content
pars_inf: Fraction of sites that are parsimony informative
total_exon_length: Total exon length
less_than_cutoff: Logical flag indicating whether alignment passed the minimum exon length cutoff or not
alignment: The original input alignment