IQ-TREE - Efficient phylogenomic software by maximum likelihood

  •        24

The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis. As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL.

http://www.iqtree.org
https://github.com/Cibiv/IQ-TREE

Tags
Implementation
License
Platform

   




Related Projects

mobisys2018_nexmon_software_defined_radio - Proof of concept project for operating Broadcom Wi-Fi chips as arbitrary signal transmitters similar to software-defined radios (SDRs)

  •    Shell

NEX_WRITE_TEMPLATE_RAM (426) writes arbitrary data into Template RAM that stores the raw IQ samples that we may transmit. The ioctl's payload contains (1) an int32 value indicating the offset where data should be written in Template RAM in bytes, (2) an int32 value indicating the length of the data that should be written and (3) the IQ samples as array of IQ values, where I (inphase components) and Q (quadrature components) are stored as int16 numbers. NEX_SDR_START_TRANSMISSION (427) that triggers the transmission of IQ samples. The ioctl's payload contains (1) an int32 value indicating the number of samples to transmit, (2) an int32 value indicating the offset where the signal starts in Template RAM, (3) an int32 value indicating a chanspec (channel number, bandwidth, band, ...), (4) an int32 value indicating the power index (lower value means higher output power), and (5) an int32 value indicating whether to loop over the IQ samples or transmit them only once.

ancestry - Organise ActiveRecord model into a tree structure

  •    Ruby

Ancestry is a gem that allows the records of a Ruby on Rails ActiveRecord model to be organised as a tree structure (or hierarchy). It uses a single database column, using the materialised path pattern. It exposes all the standard tree structure relations (ancestors, parent, root, children, siblings, descendants) and all of them can be fetched in a single SQL query. Additional features are STI support, scopes, depth caching, depth constraints, easy migration from older gems, integrity checking, integrity restoration, arrangement of (sub)tree into hashes and different strategies for dealing with orphaned records. In version 1.2.0 the acts_as_tree method was renamed to has_ancestry in order to allow usage of both the acts_as_tree gem and the ancestry gem in a single application. method acts_as_tree will continue to be supported in the future.

elasticsearch-learning-to-rank - Plugin to integrate Learning to Rank (aka machine learning for better relevance) with Elasticsearch

  •    Java

Rank Elasticsearch results using tree based (LambdaMART, Random Forest, MART) and linear models. Models are trained using the scores of Elasicsearch queries as features. You train offline using tooling such as with xgboost or ranklib. You then POST your model to a to Elasticsearch in a specific text format (the custom "ranklib" language, documented here). You apply a model using this plugin's ltr query. See blog post and the full demo (training and searching).Models are stored using an Elasticsearch script plugin. Tree-based models can be large. So we recommend increasing the script.max_size_in_bytes setting. Don't worry, just because tree-based models are verbose, doesn't nescesarilly imply they'll be slow.

XOM - XML object model in Java

  •    Java

XOM is a new XML object model. It is a tree-based API for processing XML with Java that strives for correctness, simplicity, and performance, in that order.

Apache Axiom - XML object model supporting deferred parsing

  •    Java

Apache Axiom is an XML object model supporting deferred parsing.


RubyTree - A General Purpose Tree Data Structure for Ruby

  •    Ruby

RubyTree is a pure Ruby implementation of the generic tree data structure. It provides a node-based model to store named nodes in the tree, and provides simple APIs to access, modify and traverse the structure. The implementation is node-centric, where individual nodes in the tree are the primary structural elements. All common tree-traversal methods (pre-order, post-order, and breadth-first) are supported.

angular-bootstrap-nav-tree - An AngularJS directive that creates a Tree based on a Bootstrap "nav" list

  •    CoffeeScript

This is a Tree directive for Angular JS apps that use Bootstrap CSS. The style is completely Bootstrap because the tree is actually just a Bootstrap "nav" list, with a few changes: Indentation is added, expand/collapse icons are added, and Angular CSS animations are used during expand/collapse.

The Family Tree project

  •    

The Family Tree Project is a collection of libraries and tools to manage Genealogical data. We will be providing a GEDCOM Library for managing GEDCOM data, a "Family Tree" Framework, whiich will provide a rich object model for managing Genealogical data an ASP.NET MVC applic...

Tree Factory

  •    PHP

Tree Factory is a set of PHP classes for manipulating hierarchical tree structures stored in MySQL databases. So far the nested sets tree model is in a mid-alpha stage of development. Other models will follow--all with compatible APIs. Req MySQL 4.1.2

asemon

  •    

Tool for monitoring Sybase products (ASE, RS, IQ, RAO) Supported versions : ASE : from 12.5.0.3 to 15.7 RS : from 12.6 to 15.7 IQ : from 12.6 to 15.4 RAO : from 12.5 to 15.5 Two components : - asemon_logger : the java agent which collects indicators and archive them in a database - asemon_report : the web client, written in PHP, used to query the indicator's database (use quot;Filesquot; menu to download this component) See : https://sourceforge.net/apps/mediawiki/asemon/index.php?title=Ma

jetstream-ios - An elegant model framework written in Swift

  •    Swift

Jetstream for iOS is an elegant MVC model framework written in Swift. It includes support for the Jetstream Sync protocol to sync local and remote models. Out of the box, it has a single Websocket transport adapter with the ability to add custom transport adapters.Jetstream works with two basic concepts: All your model objects extend from the superclass ModelObject and one of your ModelObject instances will be the root for your model tree which is wrapped by a Scope.

laravel-admin - Build a full-featured administrative interface in ten minutes

  •    PHP

⛵laravel-admin is administrative interface builder for laravel which can help you build CRUD backends just with few lines of code. Inspired by SleepingOwlAdmin and rapyd-laravel.

Gaussian Mixture Model and Regression

  •    C

GMM-GMR is a light package of functions in C/C++ to compute Gaussian Mixture Model (GMM) and Gaussian Mixture Regression (GMR). It allows to encode any dataset in a GMM, and GMR can then be used to retrieve partial data by specifying the desired inputs.

tree-grid-directive - Need one or more maintainer for this! comment or email me if you are interested

  •    Javascript

A grid to display data in tree structure by using Angular and Bootstrap. Feel free to whatever you want to do with it.

laravel-nestedset - Effective tree structures in Laravel 4-5

  •    PHP

This is a Laravel 4-5 package for working with trees in relational databases. The nested set model is to number the nodes according to a tree traversal, which visits each node twice, assigning numbers in the order of visiting, and at both visits. This leaves two numbers for each node, which are stored as two attributes. Querying becomes inexpensive: hierarchy membership can be tested by comparing these numbers. Updating requires renumbering and is therefore expensive.

sketch-rnn - Multilayer LSTM and Mixture Density Network for modelling path-level SVG Vector Graphics data in TensorFlow

  •    Python

This version of sketch-rnn has been depreciated. Please see an updated version of sketch-rnn, which is a full generative model for vector drawings. Implementation multi-layer recurrent neural network (RNN, LSTM GRU) used to model and generate sketches stored in .svg vector graphic files. The methodology used is to combine Mixture Density Networks with a RNN, along with modelling dynamic end-of-stroke and end-of-content probabilities learned from a large corpus of similar .svg files, to generate drawings that is simlar to the vector training data.

DeepJ - A deep learning model for style-specific music generation.

  •    Python

Recent advances in deep neural networks have enabled algorithms to compose music that is comparable to music composed by humans. However, few algorithms allow the user to generate music with tunable parameters. The ability to tune properties of generated music will yield more practical benefits for aiding artists, filmmakers, and composers in their creative tasks. In this paper, we introduce DeepJ - an end-to-end generative model that is capable of composing music conditioned on a specific mixture of composer styles. Our innovations include methods to learn musical style and music dynamics. We use our model to demonstrate a simple technique for controlling the style of generated music as a proof of concept. Evaluation of our model using human raters shows that we have improved over the Biaxial LSTM approach. Clone Python MIDI (https://github.com/vishnubob/python-midi) cd python-midi then install using python3 setup.py install.

pixel-cnn - Python3 / Tensorflow implementation of PixelCNN++, as described in "PixelCNN++: A PixelCNN Implementation with Discretized Logistic Mixture Likelihood and Other Modifications"

  •    Python

PixelCNN++: A PixelCNN Implementation with Discretized Logistic Mixture Likelihood and Other Modifications, by Tim Salimans, Andrej Karpathy, Xi Chen, Diederik P. Kingma, and Yaroslav Bulatov. This code supports multi-GPU training of our improved PixelCNN on CIFAR-10 and Small ImageNet, but is easy to adapt for additional datasets. Training on a machine with 8 Maxwell TITAN X GPUs achieves 3.0 bits per dimension in about 10 hours and it takes approximately 5 days to converge to 2.92.

django-mptt - Utilities for implementing a modified pre-order traversal tree in django.

  •    Python

Utilities for implementing Modified Preorder Tree Traversal with your Django Models and working with trees of Model instances. MPTT is a technique for storing hierarchical data in a database. The aim is to make retrieval operations very efficient.