All Projects → evogytis → baltic

evogytis / baltic

Licence: GPL-3.0 license
baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

Programming Languages

python
139335 projects - #7 most used programming language

Projects that are alternatives of or similar to baltic

pastml
Ancestor character reconstruction and visualisation for rooted phylogenetic trees
Stars: ✭ 15 (-75%)
Mutual labels:  visualisation, phylogenetics
SubstitutionModels.jl
Biological Sequence Substitution Models for Julia
Stars: ✭ 13 (-78.33%)
Mutual labels:  phylogenetics
iterated-function-systems
Iterated Function Systems fractals with OCaml.
Stars: ✭ 33 (-45%)
Mutual labels:  visualisation
r2g
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
Stars: ✭ 49 (-18.33%)
Mutual labels:  phylogenetics
TrajSuite
TrajSuite is a cross-platform Java application that provides a suite of trajectory data-mining and visualisation features.
Stars: ✭ 15 (-75%)
Mutual labels:  visualisation
Animations-with-Matplotlib
Using the matplotlib library to create some interesting animations.
Stars: ✭ 42 (-30%)
Mutual labels:  visualisation
Simulizer
A MIPS (R3000) Processor Emulator and Visualisation tool
Stars: ✭ 28 (-53.33%)
Mutual labels:  visualisation
downsample
Collection of several downsampling methods for time series visualisation purposes.
Stars: ✭ 50 (-16.67%)
Mutual labels:  visualisation
scenery
Flexible VR Visualisation for Volumetric and Geometric Data on the Java VM, powered by Kotlin and Vulkan
Stars: ✭ 107 (+78.33%)
Mutual labels:  visualisation
q2-qemistree
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
Stars: ✭ 23 (-61.67%)
Mutual labels:  phylogenetics
ltr-tools
Set of command line tools for Learning To Rank
Stars: ✭ 13 (-78.33%)
Mutual labels:  visualisation
BigComputeLabs
Big Compute Learning Labs
Stars: ✭ 19 (-68.33%)
Mutual labels:  visualisation
booster
booster.c3bi.pasteur.fr
Stars: ✭ 22 (-63.33%)
Mutual labels:  phylogenetics
midi-recorder
🎹 The easiest way to record MIDI. No install. Automatically records.
Stars: ✭ 38 (-36.67%)
Mutual labels:  visualisation
chord-transitions
Transitioning Chord Diagram Demo with Angular/D3
Stars: ✭ 38 (-36.67%)
Mutual labels:  visualisation
Game-Animation
A python tool to visualise game animations
Stars: ✭ 74 (+23.33%)
Mutual labels:  visualisation
NBA-Shot-Charts
Create NBA shot charts using data scrapped from stats.nba.com and R package ggplot2.
Stars: ✭ 33 (-45%)
Mutual labels:  visualisation
workshop
Workshop: Micromagnetics with Ubermag
Stars: ✭ 19 (-68.33%)
Mutual labels:  visualisation
notebook-examples
Example notebooks showing how to work with ECMWF services and data
Stars: ✭ 103 (+71.67%)
Mutual labels:  visualisation
RNeXML
Implementing semantically rich NeXML I/O in R
Stars: ✭ 12 (-80%)
Mutual labels:  phylogenetics

Build Status

baltic

baltic is a Python library for parsing phylogenetic trees. It takes newick, Nexus or nextstrain JSON trees and allows you to manipulate, explore and visualise them. baltic stands for Backronymed Adaptable Lightweight Tree Import Code if you like that sort of thing.


Installation

Use package manager pip to install baltic:

pip install baltic

Usage

import baltic as bt

# When called with a tree string the `make_tree()` function return a baltic tree object:

treeString='((A:1.0,B:2.0):1.0,C:3.0);'
myTree = bt.make_tree(treeString)

# Otherwise you can import trees from newick, nexus or nextstrain JSON files

newickPath='/Users/myUsername/tree.newick'
myTree = bt.loadNewick(newickPath)

nexusPath='/Users/myUsername/tree.nex'
myTree = bt.loadNexus(nexusPath, absoluteTime = False)

nextstrainPath='https://nextstrain.org/charon/getDataset?prefix=/dengue/denv1'
myTree, myMeta = bt.loadJSON(nextstrainPath)

Copyright 2016 Gytis Dudas. Licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Note that the project description data, including the texts, logos, images, and/or trademarks, for each open source project belongs to its rightful owner. If you wish to add or remove any projects, please contact us at [email protected].