arzwa/newicktree.jl

Newick formatted (phylogenetic) trees

NewickTree.jl

Read a newick tree to a tree data structure. The resulting data structure supports the AbstractTrees.jl interface.

Reading trees

using NewickTree
t = readnw("((A:1.2,B:1.4)86:0.2,C:0.6);")
print_tree(t)

((A:1.2,B:1.4)86.0:0.2,C:0.6);
├─ (A:1.2,B:1.4)86.0:0.2;
│  ├─ A:1.2;
│  └─ B:1.4;
└─ C:0.6;

Use readnw(readline("your_file.nw")) to read a newick tree from a file. Use readnw.(readlines("your_file.nw")) to read a vector of trees from a file with a newick tree on each line. To read a single newick string one can also use

t = nw"((A:1.2,B:1.4)86:0.2,C:0.6);"

((A:1.2,B:1.4)86.0:0.2,C:0.6);

Subtrees can be accessed by indexing

t[1]

(A:1.2,B:1.4)86.0:0.2;

Some simple recursive tree traversals are implemented

postwalk(t)
prewalk(t)

5-element Vector{NewickTree.Node{UInt16, NewickTree.NewickData{Float64, String}}}:
 ((A:1.2,B:1.4)86.0:0.2,C:0.6);
 (A:1.2,B:1.4)86.0:0.2;
 A:1.2;
 B:1.4;
 C:0.6;

There are also the following self-explanatory functions:

getleaves(t)
getroot(t)
getlca(t, "A", "B")  # get last common ancestor

(A:1.2,B:1.4)86.0:0.2;

Functions from AbstractTrees can also be used, for instance

using AbstractTrees
collect(Leaves(t))
collect(PostOrderDFS(t))

5-element Vector{NewickTree.Node{UInt16, NewickTree.NewickData{Float64, String}}}:
 A:1.2;
 B:1.4;
 (A:1.2,B:1.4)86.0:0.2;
 C:0.6;
 ((A:1.2,B:1.4)86.0:0.2,C:0.6);

Writing trees

nwstr converts a tree data structure that implements the required functions (see below) to a Newick string:

nwstr(t)

"((A:1.2,B:1.4)86.0:0.2,C:0.6);"

writenw uses this to write to a stream or file.

io = IOBuffer()
writenw(io, t)
String(take!(io))

"((A:1.2,B:1.4)86.0:0.2,C:0.6);"

Plotting trees

There is a Plots.jl recipe defined in NewickTree, the following should work

using Plots
t = nw"(((((((Scer,Spar),Smik),Skud),Sbay),Scas),Sklu),Calb);"
plot(t, transform=true);

this composes nicely with all other functionality in Plots.jl, for instance:

plot(plot(t, transform=true), plot(randn(100)));

Further details

Note that trees should adhere to the Newick standard, they should end with a semicolon and can only contain (1) leaf names, (2) support values or internal names and (3) branch lengths as node information. Failure to provide a valid Newick string will trigger an error:

try
    t = readnw("((A:1.2,B:1.4)86:0.2,C:0.6)")
catch ex
    @show ex
end

"Malformed Newick string '((A:1.2,B:1.4)86:0.2,C:0.6)' (no trailing semicolon?)"

The tree data structure is pretty straightforward, with nodes storing the following fields:

fieldnames(typeof(t))

(:id, :data, :parent, :children)

Support for writing other tree structured data to Newick strings

Any data structure that implements the AbstractTrees interface (i.e. defines AbstractTrees.children) can be written to a Newick structure provided several functions are defined. For example:

t = (((1,2),3),(4,5))
NewickTree.isleaf(::Int) = true
NewickTree.isleaf(::Tuple) = false
print_tree(t)

(((1, 2), 3), (4, 5))
├─ ((1, 2), 3)
│  ├─ (1, 2)
│  │  ├─ 1
│  │  └─ 2
│  └─ 3
└─ (4, 5)
   ├─ 4
   └─ 5

This enables us to use the nwstr and writenw functions

s = nwstr(t)

"(((1,2),3),(4,5));"

now we can read the Newick string

n = readnw(s)
print_tree(n)

(((1,2),3),(4,5));
├─ ((1,2),3);
│  ├─ (1,2);
│  │  ├─ 1;
│  │  └─ 2;
│  └─ 3;
└─ (4,5);
   ├─ 4;
   └─ 5;

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newicktree.jl's Issues

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hclust to Newick conversion

I found your code in this comment to be a lifesaver, enabling interoperability of Clustering.jl and Phylo.jl

JuliaStats/Clustering.jl#209 (comment)

Would it make sense to include such a function in NewickTree.jl?

Support extended Newick?

It seems the package cannot read extended Newick format trees?

I'm having trouble in particular reading trees stored in RFAM (https://docs.rfam.org/en/latest/api.html?highlight=nhx#tree-data). For example,

http://rfam.org/family/RF00360/tree/

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