Input/Output

MolecularEvolution.write_nexus Function

write_nexus(fname::String,tree::FelNode)

Writes the tree as a nexus file, suitable for opening in eg. FigTree. Data in the node_data dictionary will be converted into annotations. Only tested for simple node_data formats and types.

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MolecularEvolution.newick Function

newick(root)

Returns a newick string representation of the tree.

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MolecularEvolution.read_newick_tree Function

read_newick_tree(treefile)

Reads in a tree from a file, of type FelNode

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MolecularEvolution.populate_tree! Function

populate_tree!(tree::FelNode, starting_message, names, data; init_all_messages = true, tolerate_missing = 1, leaf_name_transform = x -> x)

Takes a tree, and a starting_message (which will serve as the memory template for populating messages all over the tree). starting_message can be a message (ie. a vector of Partitions), but will also work with a single Partition (although the tree) will still be populated with a length-1 vector of Partitions. Further, as long as obs2partition is implemented for your Partition type, the leaf nodes will be populated with the data from data, matching the names on each leaf. When a leaf on the tree has a name that doesn't match anything in names, then if

• tolerate_missing = 0, an error will be thrown

• tolerate_missing = 1, a warning will be thrown, and the message will be set to the uninformative message (requires identity!(::Partition) to be defined)

• tolerate_missing = 2, the message will be set to the uninformative message, without warnings (requires identity!(::Partition) to be defined)

A renaming function that can eg. strip tags from the tree when matching leaf names with names can be passed to leaf_name_transform

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MolecularEvolution.read_fasta Function

read_fasta(filepath::String)

Reads in a fasta file and returns a tuple of (seqnames, seqs).

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MolecularEvolution.write_fasta Function

write_fasta(filepath::String, sequences::Vector{String}; seq_names = nothing)

Writes a fasta file from a vector of sequences, with optional seq_names.

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