rectree2svg 2.2.0

Read phylogenetic tree(s) in newick, phyloxml or recPhyloXML file and build a svg representation of the tree(s).
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137

# rectree2svg

[![rectree2svg at crates.io](https://img.shields.io/crates/v/rectree2svg.svg)](https://crates.io/crates/rectree2svg)



Build a svg representation of a phylogenetic reconciled (or not) tree with events (loss, duplication, speciation, transfer).

Read a recphyloxml file:  create a svg representation of the  gene tree(s) and the associated species tree.

Read a newick (rooted tree only) or phyloxml file: create a svg representation of the gene tree only .


Keywords:  phylogeny, reconciled trees, phylogenetic trees

# Formats:

phyloXML, recPhyloXML, rooted newick ( NHX balises will not be considered ).

# Output examples

multiple genes reconciliation recphyloxml:

https://raw.githubusercontent.com/simonpenel/rectree2svg/9244f3136961f909fd7b33818f0a220e3f32c880/tree2svg.example.svg


single gene reconciliation in recphyloxml:

https://raw.githubusercontent.com/simonpenel/rectree2svg/9244f3136961f909fd7b33818f0a220e3f32c880/FAM000696_reconciliated_recphyloxml.svg

the same gene reconciliation in phyloxml:

https://raw.githubusercontent.com/simonpenel/rectree2svg/9244f3136961f909fd7b33818f0a220e3f32c880/FAM000696_reconciliated_xml.svg


# Install:

rectree2svg is written in Rust. The code is managed using Cargo and published on crates.io.

Install cargo:

    curl https://sh.rustup.rs -sSf | sh

or for Windows see  https://doc.rust-lang.org/cargo/getting-started/installation.html

Once Cargo is installed just open a terminal and type:

    cargo install rectree2svg

You may as well install from the sources. Clone or download  the sources here https://github.com/simonpenel/rectree2svg and type:

    cargo build --release
    target/release/rectree2svg -h

# Run the binary:
Read a newick, phyloxml or recPhyloXML file and create a svg.

Format is guessed according to filename (default is newick)

Usage:

    rectree2svg -f input file [-b][-c config file][-g #][-h][-i][-I][-l factor][-o output file][-p][-r ratio][-s][-v]

    -b : open svg in browser
    -c configfile: use a configuration file    
    -F phylo/recphylo: force format phyloXML/recPhyloXML
    -g <n> : display the gene #n in phyloxml style (no species tree)
    -h : help
    -i : display internal gene nodes
    -I : display internal species nodes
    -L : display as landscape
    -l factor: use branch length, using the given factor
    -o outputfile : set name of output file
    -p : build a phylogram   
    -r ratio : set the ratio between width of species and gene tree.
               Default 1.0, you usualy do not need to change it.
    -s : drawing species tree only
    -v : verbose

`Input format is guessed according to the file name extension:`

    - .xml         => phyloxml
    - .phyloxml    => phyloXML
    - .recphyloxml => recPhyloXML
    - .recPhyloXML => recPhyloXML
    - .recphylo    => recPhyloXML
    - any other    => newick

You will find several input file examples in newick_examples, recphylo_examples and xml_examples directories.


# Configuration file:

You may configure some of the features of the svg with the -c option.

The default values are the values of the "config_default.txt" file.

Modify the default values and save it into  "my_config.txt" then type:

```
rectree2svg -f recphylo_examples/FAM000600_reconciliated_big.recphylo -c my_config.txt -b

```


# Using the API:


rectree2svg use the light_phylogeny crate:

https://crates.io/crates/light_phylogeny


# Source documentation

See Rust documentation : https://docs.rs/rectree2svg/

# recPhyloXML documentation

See http://phylariane.univ-lyon1.fr/recphyloxml/

recPhyloXML paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198865/

# phyloXML documentation

See: http://www.phyloxml.org/

phyloXML paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774328/

# Under development:

- Allow 2/3 reconciliation levels (host/species/gene)



# Licence
CECILL: https://choosealicense.com/licenses/cecill-2.1/