MCView creates a Shiny app facilitating interactive exploration and annotation of Metacell models.

Easel is an ANSI C code library developed by the Eddy/Rivas laboratory at Harvard. Easel supports our work on computational analysis of biological sequences using probabilistic models. Easel is used by HMMER, the profile hidden Markov model software that underlies several protein and DNA sequence family databases such as Pfam, and by Infernal, the profile stochastic context-free grammar software that underlies the Rfam RNA family database. Easel aims to make similar applications more robust and easier to develop, by providing a set of reusable, documented, and well-tested functions.

hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains, like HK27me3. The input data can be in BAM format, or in a tab-delimited 'reads per bin' format described below. The output is a BED formatted file the lists the enriched domains and their posterior probabilities.

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

Control-FREEC automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. The control (matched normal) sample is optional for whole genome sequencing data but mandatory for whole exome or targeted sequencing data. For whole genome sequencing data analysis, the program can also use mappability data (files created by GEM).

Scriabin aims to provide a comprehensive view of cell-cell communication (CCC). It achieves this without requiring subsampling or aggregation.

Bioparser is a C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.

tsinfer is a Python package to infer an ARG in tree sequence format from large quantities of phased DNA sequence data in VCF Zarr format (see the usage documentation for how to convert data from a VCF into a suitable input format).

This package provides the Python library for the BGEN format (specifications 1.2 and 1.3).

This packages provides a collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.

This package contains the following programs: bamcollate2, bammarkduplicates, bammaskflags, bamrecompress, bamsort, bamtofastq.

Terraphast takes a .nkw file in Newick format and a genes/sites file, which denotes whether (1) or not (0) gene i is present in species j.

Program output states some imput data properties, the species whose leaf edge is used as a new tree root, and the resulting supertree in compressed newick format.

scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.

This package provides a tool to download or view data in the cloud environments of ICGC.

msprime is a population genetics simulator based on tskit. Msprime can simulate random ancestral histories for a sample of individuals (consistent with a given demographic model) under a range of different models and evolutionary processes. Msprime can also simulate mutations on a given ancestral history (which can be produced by msprime or other programs supporting tskit) under a variety of genome sequence evolution models.

This package provides the reference implementation of CGP workflow for CaVEMan SNV analysis.

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.

Key features of IQ-TREE:

• Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood;

• An ultrafast bootstrap approximation (UFBoot) to assess branch supports;

• An ultrafast and automatic model selection (ModelFinder);

• A flexible simulator (AliSim) which can simulate sequence alignments under more realistic models than Seq-Gen and INDELible;

• Several fast branch tests like SH-aLRT and aBayes test and tree topology tests like the approximately unbiased (AU) test.

This package provides IQ-TREE version 3.

A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes. It includes ten models added to the metagenome mode:

• Acanthamoeba polyphaga mimivirus

• Paramecium bursaria Chlorella virus

• Acanthocystis turfacea Chlorella virus

• VirSorter2's NCLDV gene model

• Topaz (genetic code 15)

• Agate (genetic code 15)

• Gut phages (genetic code 15)

• Gut phages (genetic code 11) x 5

Anvi’o is a comprehensive platform that brings together many aspects of today’s computational strategies of data-enabled microbiology, including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.

piqtree is a Python package that exposes selected IQ-TREE capabilities within Python, using the cogent3 library as the interface.

piqtree is implemented with the goals of:

• making the individual high-performance components of IQ-TREE available within Python, enabling the community to take advantage of these routines.

• facilitating exploratory analyses by leveraging cogent3's capabilities to provide a rich user experience in interactive Jupyter notebooks, e.g. trivial parallelisation across collections of alignments.

• code using piqtree apps should be easy to understand.