write_partitioned_alignments2: Write alignment partitions as separate alignment files for...

In EvoPhylo: Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

Write alignment partitions as separate alignment files for various data types

Description

Write alignment partitions as separate alignment files for various data types

Usage

write_partitioned_alignments2(
  x,
  cluster_df,
  partition_file,
  in_format = NULL,
  in_type = NULL,
  out_file,
  out_type = "standard"
)

Arguments

x	concatenated alignment file in Nexus or Phyllip format read directly from local directory
cluster_df	cluster partitions as outputted by make.clusters
partition_file	name of text file with user provided partitions, with names and start&end positions
in_format	Format of the input alignment file. One of "phylip", "interleaved", "sequential", "clustal", "fasta", or "nexus", or any unambiguous abbreviation. Passed to phangorn::read.phyDat.
in_type	Type of input sequences. One of "DNA", "AA", "CODON" or "USER". Passed to phangorn::read.phyDat.
out_file	Path to save the alignments. If out_file = "example.nex", files will be saved as "example_part1.nex", "example_part2.nex", etc.
out_type	Output format type. One of "dna" (default), "protein", "standard", or "continuous".

Value

No return value. This function is called for its side effect of writing alignment files to disk.

See Also

write_partitioned_alignments for the older version supporting morphological data only.

Examples

# Load example phylogenetic data matrix
data("characters")

# Create distance matrix
Dmatrix <- get_gower_dist(characters)

# Find optimal partitioning scheme using PAM under k=3 partitions
cluster_df <- make_clusters(Dmatrix, k = 3)

# Write morphological partitions into multiple Nexus files
## Not run: write_partitioned_alignments2(x = "characters.nex",
                             cluster_df = cluster_df,
                             out_file = "test", out_type = "standard")
## End(Not run)

# Write to molecular partitions into multiple Phyllip files
## Not run: write_partitioned_alignments2(x = "alignments.phy",
                             partition_file = "sorted_partitions_50genes.txt",
                             in_format = "phylip", in_type = "dna",
                             out_file = "test", out_type = "dna")
## End(Not run)

EvoPhylo documentation built on Aug. 27, 2025, 5:11 p.m.