clonalframeml

Efficient Inference of Recombination in Whole Bacterial Genomes

ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes. ClonalFrameML was created by Xavier Didelot and Daniel Wilson. ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences. It is able to compare hundreds of whole genomes in a matter of hours on a standard Desktop computer. There are three main outputs from a run of ClonalFrameML: a phylogeny with branch lengths corrected to account for recombination, an estimation of the key parameters of the recombination process, and a genomic map of where recombination took place for each branch of the phylogeny.

merecat

Embedded web server

This is a simple web server based on Jef Poskanzer's thttpd. It supports all basic features required for most use-cases. The most prominent features are probably HTTPS, using OpenSSL, PHP, multiple servers with HTTP redirect support, redirect from HTTP to HTTPS, virtual hosts, and the URL-traffic-based throttling.

php-symfony-polyfill

Symfony polyfills backporting features to lower PHP versions

The Symfony Polyfill project backports features found in the latest PHP versions and provides compatibility layers for some extensions and functions. It is intended to be used when portability across PHP versions and extensions is desired.

node-prosemirror-view

ProseMirror's view component

This is a core module of ProseMirror. ProseMirror is a well-behaved rich semantic content editor based on contentEditable, with support for collaborative editing and custom document schemas.

g++-12-multilib

GNU C++ compiler (multilib support)

This is the GNU C++ compiler, a fairly portable optimizing compiler for C++.

node-typanion

Static and runtime type assertion library with no dependencies

Compared to yup, Typanion has a better inference support for TypeScript.