Code and services
In no particular order:- alv: an alignment viewer
- View your DNA or protein multiple-sequence alignments right at your command line. No need to launch a
GUI!
Features:
- Command-line based, no GUI, so easy to script viewing of many (typically small) MSAs.
- Reads alignments in FASTA, Clustal, PHYLIP, and Stockholm formats.
- Output is formatted to suit your terminal. You can also set the alignment width with option `-w`.
- Can color alignments of coding DNA by codon's translations to amino acids.
- Guesses sequence type (DNA/RNA/AA/coding) by default. You can override with option `-t`.
- Order sequence explicitly, alphabetically, or by sequence similarity.
- Restrict coloring to where you don't have indels or where there is a lot of conservation.
- The BESST scaffolder
- A fast scaffolder with great accuracy, built on a method for unbiased estimation of contig distance.
- FastPhylo
- FastPhylo is software project containing the implementations of the algorithms "Fast Computation of Distance Estimators", "Fast Neighbor Joining", and more.
There is MPI support for distance calculations (fastprot, fastdist). Related publications:
- Elias & Lagergren, Fast Computation of Distance Estimators, BMC Bioinformatics, 2007.
- Elias & Lagergren, Fast Neighbor Joining, Theoretical Computer Science, 2009.
- Khan et al, FastPhylo: Fast tools for phylogenetics, BMC Bioinformatics, 2013.
- PrIME/jPrIME
- Bayesian estimation of gene family phylogenies and
duplication/loss parameters, et.c., with a species tree used as
prior information.
Note the wiki with documentation! (And forget about old web pages on SourceForge, Google Code, and our SciLifeLab domain...)
A downloadable jar is also here: jprime-0.3.7.jar.
- VMCMC
- A tool for visualising and analysing MCMC traces.
VMCMC takes as input Markov Chain Monte Carlo (MCMC) traces from various softwares, visualize it, and calculates and displays the statistical properties such as burnin and convergence tests.
- Ali et al., VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces, BMC Bioinformatics, 2017.
- GenFamClust (BitBucket)
- A method for clustering proteins/genes based on similarity and gene order information.
- Ali, Muhammad, and Arvestad, GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm, BMC Evol Biol, 2016.
- PrIMETV
-
A tool for visualizing gene family evolution
within a species phylogeny. This version was implemented by José Fernández Navarro.
A web service for this tool is unfortunately currently out of service, but is being resurrected by Alexandra Onegård.
- Sennblad et al., primetv: a viewer for reconciled trees, BMC Bioinformatics, 2007.
- Excap
- Choosing informative markers in DNA sequences.
- modelestimator
- Estimate your own amino acid rate matrices and produce output for PAML and FASTA. This program implements a robust method which is described in a JME paper.
- RefSense
- For those who rather use shell tools than web services, I have brought some of the features from Web RefSense over in a set of scripts. You can now easily have PubMed at your fingertips by using RefSense.