The is an introductory course that is aimed at students who will need to preform phylogenetic analyses in their work, but who have little or no experience with phylogenetic analyses.
github.com - A simple, extensible, Perl script for producing figures of large phylogenetic trees.
While there are many other tree drawing programs, slacTree was originally written in 2009 to fill a need for producing publication quality figures of circular...
christophergandrud.github.io - Mike Bostock’s D3.js is great for creating interactive network graphs with JavaScript. The d3Network package makes it easy to create these network graphs from R. The main idea is that you should able to take...
https://www.onezoom.org/ - An interactive map of the evolutionary links between all living things known to science. Discover your favourites, see which species are under threat, and be amazed by the diversity of life on earth.
github.com - SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically...
lbbe.univ-lyon1.fr - SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parents and progeny of each sex) to infer autosomal and sex-linked genes (genes located on the non recombining part of sex chromosomes).
How does SEX-DETector...
github.com - chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons.
USAGE:
-query: sequence A in fasta format
-db: sequence B in fasta format
-out: output matrix
-kmer Integer: k>1...
github.com - Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs...
When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s group.
Again, running spades.py will show you the...
