EvoPhylo (version 0.3.5)

write_partitioned_alignments2: 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"
)

Value

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

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".

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
if (FALSE) write_partitioned_alignments2(x = "characters.nex",
                             cluster_df = cluster_df,
                             out_file = "test", out_type = "standard")

# Write to molecular partitions into multiple Phyllip files
if (FALSE) write_partitioned_alignments2(x = "alignments.phy",
                             partition_file = "sorted_partitions_50genes.txt",
                             in_format = "phylip", in_type = "dna",
                             out_file = "test", out_type = "dna")