BOL: Related items

When Thousands of Bacterial Genomes Become One Giant Map

LEGE — Thu, 27 Aug 2026 10:56:47 -0500

Imagine trying to understand a city by studying just one house.

You might learn a lot about that house—the rooms, the doors, the furniture—but you would miss the bigger story: the streets, the neighborhoods, and all the ways the city changes from one place to another.

Something similar happens when scientists study bacterial genomes one at a time.

Over the past decade, researchers have collected thousands of bacterial genomes. These genomes contain an enormous amount of information about how bacteria survive, adapt, and evolve. But comparing thousands of individual genomes can quickly become a computational maze.

That is where PANORAMA enters the story.

Developed by Jérôme Arnoux and colleagues, PANORAMA is a computational tool designed to explore bacterial pangenomes—the complete collection of genetic possibilities found across a species or group of related organisms. Instead of looking at every genome as an isolated object, the approach represents their shared and variable genetic features as a graph.

Think of this graph as a giant subway map.

Some stations appear on almost every route. These represent genes that are highly conserved. Other stations appear only on certain routes, representing genes that some bacteria possess while others do not. By looking at the entire network, scientists can begin to see not just *what genes exist*, but how they are organized and how biological systems are distributed across populations.

The researchers put PANORAMA to the test using 941 genomes of Pseudomonas aeruginosa, a bacterium important in human health. They used the tool to investigate biological systems, including bacterial defense mechanisms against viruses known as bacteriophages. They then expanded the analysis to more than 6,000 genomes from four Enterobacteriaceae species.

The result is more than a faster way to process data.

PANORAMA allows researchers to ask a bigger question: What can an entire microbial species do, genetically speaking?

By comparing pangenomes, the researchers could identify systems shared between species as well as distinctive features. They could also find recurring genomic locations where genetic material is inserted—clues that may reveal common evolutionary processes.

And this is perhaps the most exciting part of the story.

Every bacterial genome is like a page in a huge evolutionary book. Until recently, reading thousands of those pages together was difficult. PANORAMA provides a way to turn those pages into a map, allowing scientists to see patterns that might disappear when each genome is studied separately.

The study, published in PLOS Computational Biology in July 2026, presents PANORAMA as a foundation for large-scale comparative pangenomics. The software and accompanying analysis resources are openly available, giving other researchers the opportunity to explore microbial diversity themselves.

So the story is not really about one bacterium or one genome.

It is about changing the way we look at life.

Instead of asking, “What is inside this genome?”, scientists can increasingly ask, “What is the full genetic landscape of this species—and how did it become this way?”

And sometimes, when you stop looking at one house and finally see the whole city, the most interesting discoveries are hiding in the streets between them.

Read more at https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013856

Phylogenetic for Bioinformatics

Jitendra Narayan — Tue, 16 Jul 2013 03:50:30 -0500

Biologists estimate that there are about 5 to 100 million species of organisms living on Earth today. Evidence from morphological, biochemical, and gene sequence data suggests that all organisms on Earth are genetically related, and the genealogical relationships of living things can be represented by a vast evolutionary tree, the Tree of Life. The Tree of Life then represents the phylogeny of organisms, i. e., the history of organismal lineages as they change through time.
Every living organism contains DNA, RNA, and proteins. Closely related organisms generally have a high degree of agreement in the molecular structure of these substances, while the molecules of organisms distantly related usually show a pattern of dissimilarity. Molecular phylogeny uses such data to build a "relationship tree" that shows the probable evolution of various organisms. Not until recent decades, however, has it been possible to isolate and identify these molecular structures.
phylogenetics is the study of evolutionary relatedness among various groups of organisms (for example, species or populations), which is discovered through molecular sequencing data and morphological data matrices. In other word, Phylogenetics, the science of phylogeny, is one part of the larger field of systematics, which also includes taxonomy. Taxonomy is the science of naming and classifying the diversity of organisms Molecular phylogeny is the use of the structure of molecules to gain information on an organism's evolutionary relationships. The result of a molecular phylogenetic analysis is expressed in a so-called phylogenetic tree.

The evolutionary connections between organisms are represented graphically through phylogenetic trees. Due to the fact that evolution takes place over long periods of time that cannot be observed directly, biologists must reconstruct phylogenies by inferring the evolutionary relationships among present-day organisms.
Application of the techniques that make this possible can be seen in the very limited field of human genetics, such as the ever more popular use of genetic testing to determine a child's paternity, as well as the emergence of a new branch of criminal forensics focused on genetic evidence.
The effect on traditional scientific classification schemes in the biological sciences has been dramatic as well. Work that was once immensely labor- and materials-intensive can now be done quickly and easily, leading to yet another source of information becoming available for systematic and taxonomic appraisal. This particular kind of data has become so popular that taxonomical schemes based solely on molecular data may be encountered. Proponents even claim that taxonomy was previously based on morphology alone, which of course is utter fable.

For additional information on phylogenetics, see list of Phylogenetics Resources on the Internet.

Phylogeny and Reconstructing Phylogenetic Trees: http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html
the CBRG and Department of Statistics Phylogeny tutorial: http://www.compbio.ox.ac.uk/tutorials/phylogeny/
TUTORIAL: PHYLOGENETIC ANALYSIS USING PARSIMONY:http://home.cc.umanitoba.ca/~psgendb/GDE/phylogeny/parsimony/phylip.parsimony.html

PHYLIP: http://www.umanitoba.ca/afs/plant_science/psgendb/doc/Phylip/main.html
An Introduction to Molecular Phylogeny: http://bibiserv.techfak.uni-bielefeld.de/gcb04/tutorials/hoef-emden/GCB04Tut.pdf

How to make a phylogenetic tree: http://www.hiv.lanl.gov/content/sequence/TUTORIALS/TREE_TUTORIAL/Treetutorial.html
Phylogenetic Trees: http://cnx.org/content/m11052/latest/
Phylogeny by Ron Shamir: http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe08/lec08.pdf
Introduction to Phylogeny: http://www.utm.edu/departments/cens/biology/rirwin/391/391Phylog.htm
Lecturer notes on Phylogeny: http://www.sbc.su.se/~bens/course_material/phylocourse1/lecture2.pdf
Principles and Practice of Phylogenetic Systematics:http://www.faculty.biol.ttu.edu/Strauss/Phylogenetics/LectureNotes.htm

Inferring phylogenetic trees: http://www.cis.hut.fi/Opinnot/T-61.6070/slides2008/pres_6070.pdf

Lecture Notes

Chapter 1 - The Diversity, Classification, and Evolution of Vertebrates:http://academic.emporia.edu/mooredwi/nathist/chap1.htm

Algorithms for Phylogenetic Reconstructions:http://lectures.molgen.mpg.de/Algorithmische_Bioinformatik_WS0405/phylogeny_script.pdf

Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. For more detail : http://www.phylogeny.fr/version2_cgi/index.cgi

A Brief Tutorial on Phylogenetics
http://bioss.ac.uk/~dirk/talks/tutorial_phylogenetics.pdf

A Brief Tutorial on Phylogenetics Human Rabbit Chicken
http://bioss.ac.uk/~dirk/talks/psnup_tutorial_phylogenetics.pdf

Phylogenetic Tree Computation Tutorial Overview
http://pga.lbl.gov/Workshop/April2002/lectures/Olken.pdf

MrBayes: A program for the Bayesian inference of phylogeny
http://golab.unl.edu/teaching/SBseminar/manual.pdf

Web sites providing software for the construction of phylogenetic trees

BioEdit

Coelocanth-Fish Out of Time

Computational Biochemistry Research Group

Digital Taxonomy

Hennig 86

Hyperclean from Bioinformatics Solutions, Inc.

Memorial University of Newfoundland

Mr. Bayes

NONA

Oxford University Evolutionary Biology Group

Paleobiology Database

PAUP

Phylip Homepage

Sinauer Associates

TNT-Tree Analysis Using New Technology

Tree Base

Treefinder

Tree-Puzzle

Tree View-Taxonomy and Systematics Group at Glasgow

Washington University-List of Phylogeny Software

GEnView: A phylogeny based comparative genomics software to analyze the genetic environment of genes

Abhi — Tue, 28 Dec 2021 01:49:03 -0600

A phylogeny based comparative genomics software to analyze the genetic environment of genes. The user can select one or several taxa and provide one or several reference protein(s). Genomes and plasmids (based on user choice) will be downloaded from the NCBI Assembly/NR database and searched for the respective gene. Alternatively, custom genomes can be provided. User selected stretches (20kbp by default) of the genes genetic environment are extracted, annotated and aligned between all genomes. The sequences are then visualized, enabling comparison of synteny and gene content.

More at https://pubmed.ncbi.nlm.nih.gov/34951622/

Address of the bookmark: https://github.com/EbmeyerSt/GEnView

Tree illustrating the lack of interchromosomal rearrangement of the microchromosomes.

BioJoker — Mon, 26 Nov 2018 04:20:33 -0600

Tree illustrating the lack of interchromosomal rearrangement of the microchromosomes. No interchromosomal microchromosome fusions from the avian ancestor unless otherwise stated (macrochromosomal fusions not listed). The overall pattern of microchromosome stability and rearrangement across the species is illustrated

Jarvis et al. (2014)

Reference https://link.springer.com/article/10.1007/s00412-018-0685-6

d3Network:Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.

Jit — Fri, 06 Apr 2018 12:10:45 -0500

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 an R data frame with information about the relationships between members of a network and create full network graphs with one command.

Address of the bookmark: http://christophergandrud.github.io/d3Network/

k-mers tutorial - classification and taxonomy

Neel — Thu, 26 Aug 2021 10:28:43 -0500

DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently, discard redundant data, and count them efficiently.

More recently, we've been enthused about using k-mer based similarity measures and computing and searching k-mer-based sketch search databases for all the things.

But I haven't spent too much talking about using k-mers for taxonomy, although that has become an ahem area of interest recently, if you read into our papers a bit.

In this blog post I'm going to fix this by doing a little bit of a literature review and waxing enthusiastic about other people's work. Then in a future blog post I'll talk about how we're building off of this work in fun! and interesting? ways!

Address of the bookmark: http://ivory.idyll.org/blog/2017-something-about-kmers.html

BUSCO datasets !

Jit — Wed, 13 Jan 2021 19:44:33 -0600

The BUSCO software now directly downloads the necessary datasets, specified by the user or automatically selected.

To display all available datasets

busco --list-datasets

You can also download them manually and see a list with the number of marker genes.

Earlier versions: v3, v2, v1

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acidobacteria_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     14M
aconoidasida_odb10.2020-08-05.tar.gz               16-Oct-2020 13:19     51M
actinobacteria_class_odb10.2020-03-06.tar.gz       16-Oct-2020 13:19      8M
actinobacteria_phylum_odb10.2020-03-06.tar.gz      16-Oct-2020 13:20      9M
actinopterygii_odb10.2020-08-05.tar.gz             16-Oct-2020 13:20    173M
agaricales_odb10.2020-08-05.tar.gz                 16-Oct-2020 13:20    186M
agaricomycetes_odb10.2020-08-05.tar.gz             16-Oct-2020 13:19    152M
alphaproteobacteria_odb10.2020-03-06.tar.gz        16-Oct-2020 13:20     11M
alteromonadales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:20     18M
alveolata_odb10.2020-09-10.tar.gz                  16-Oct-2020 13:20     13M
apicomplexa_odb10.2020-09-10.tar.gz                16-Oct-2020 13:19     27M
aquificae_odb10.2020-03-06.tar.gz                  16-Oct-2020 13:19     12M
arachnida_odb10.2020-08-05.tar.gz                  16-Oct-2020 13:19    136M
archaea_odb10.2020-03-06.tar.gz                    16-Oct-2020 13:20      4M
arthropoda_odb10.2020-09-10.tar.gz                 16-Oct-2020 13:20     95M
ascomycota_odb10.2020-09-10.tar.gz                 16-Oct-2020 13:20    295M
aves_odb10.2020-09-10.tar.gz                       16-Oct-2020 13:20    465M
bacillales_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:20     10M
bacilli_odb10.2020-03-06.tar.gz                    16-Oct-2020 13:19      7M
bacteria_odb10.2020-03-06.tar.gz                   16-Oct-2020 13:20      6M
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bacteroidia_odb10.2020-03-06.tar.gz                16-Oct-2020 13:20     13M
basidiomycota_odb10.2020-09-10.tar.gz              16-Oct-2020 13:19    165M
betaproteobacteria_odb10.2020-03-06.tar.gz         16-Oct-2020 13:19     13M
boletales_odb10.2020-08-05.tar.gz                  16-Oct-2020 13:19    197M
brassicales_odb10.2020-08-05.tar.gz                16-Oct-2020 13:20    158M
burkholderiales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     16M
campylobacterales_odb10.2020-03-06.tar.gz          16-Oct-2020 13:20     14M
capnodiales_odb10.2020-08-05.tar.gz                16-Oct-2020 13:19    178M
carnivora_odb10.2020-08-05.tar.gz                  16-Oct-2020 13:19    376M
cellvibrionales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     19M
cetartiodactyla_odb10.2020-08-05.tar.gz            16-Oct-2020 13:19    407M
chaetothyriales_odb10.2020-08-05.tar.gz            16-Oct-2020 13:20    288M
chlamydiae_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:20     13M
chlorobi_odb10.2020-03-06.tar.gz                   16-Oct-2020 13:20     22M
chloroflexi_odb10.2020-03-06.tar.gz                16-Oct-2020 13:20      6M
chlorophyta_odb10.2020-08-05.tar.gz                16-Oct-2020 13:20     58M
chromatiales_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     14M
chroococcales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     27M
clostridia_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:19      6M
clostridiales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:20      6M
coccidia_odb10.2020-08-05.tar.gz                   16-Oct-2020 13:20     24M
coriobacteriales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:19     12M
coriobacteriia_odb10.2020-03-06.tar.gz             16-Oct-2020 13:20      9M
corynebacteriales_odb10.2020-03-06.tar.gz          16-Oct-2020 13:19     16M
cyanobacteria_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     17M
cyprinodontiformes_odb10.2020-08-05.tar.gz         16-Oct-2020 13:19    504M
cytophagales_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     18M
cytophagia_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:20     18M
delta-epsilon-subdivisions_odb10.2020-03-06.tar.gz 16-Oct-2020 13:19      6M
deltaproteobacteria_odb10.2020-03-06.tar.gz        16-Oct-2020 13:19      6M
desulfobacterales_odb10.2020-03-06.tar.gz          16-Oct-2020 13:20     13M
desulfovibrionales_odb10.2020-03-06.tar.gz         16-Oct-2020 13:19     17M
desulfurococcales_odb10.2020-03-06.tar.gz          16-Oct-2020 13:20      9M
desulfuromonadales_odb10.2020-03-06.tar.gz         16-Oct-2020 13:19     18M
diptera_odb10.2020-08-05.tar.gz                    16-Oct-2020 13:19    185M
dothideomycetes_odb10.2020-08-05.tar.gz            16-Oct-2020 13:19    194M
embryophyta_odb10.2020-09-10.tar.gz                16-Oct-2020 13:19    138M
endopterygota_odb10.2020-09-10.tar.gz              16-Oct-2020 13:19    190M
enterobacterales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:19     11M
entomoplasmatales_odb10.2020-03-06.tar.gz          16-Oct-2020 13:19      7M
epsilonproteobacteria_odb10.2020-03-06.tar.gz      16-Oct-2020 13:20     13M
euarchontoglires_odb10.2020-09-10.tar.gz           16-Oct-2020 13:20    728M
eudicots_odb10.2020-09-10.tar.gz                   16-Oct-2020 13:19    168M
euglenozoa_odb10.2020-08-05.tar.gz                 16-Oct-2020 13:20     10M
eukaryota_odb10.2020-09-10.tar.gz                  16-Oct-2020 13:19    100M
eurotiales_odb10.2020-08-05.tar.gz                 16-Oct-2020 13:19    211M
eurotiomycetes_odb10.2020-08-05.tar.gz             16-Oct-2020 13:19    197M
euryarchaeota_odb10.2020-03-06.tar.gz              16-Oct-2020 13:20      5M
eutheria_odb10.2020-09-10.tar.gz                   16-Oct-2020 13:20    920M
fabales_odb10.2020-08-05.tar.gz                    16-Oct-2020 13:19    184M
firmicutes_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:20      6M
flavobacteriales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:19     18M
flavobacteriia_odb10.2020-03-06.tar.gz             16-Oct-2020 13:20     18M
fungi_odb10.2020-09-10.tar.gz                      16-Oct-2020 13:19    181M
fusobacteria_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     11M
fusobacteriales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     11M
gammaproteobacteria_odb10.2020-03-06.tar.gz        16-Oct-2020 13:19     10M
glires_odb10.2020-08-05.tar.gz                     16-Oct-2020 13:19    549M
glomerellales_odb10.2020-08-05.tar.gz              16-Oct-2020 13:19    259M
halobacteria_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     18M
halobacteriales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:20     18M
haloferacales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     20M
helotiales_odb10.2020-08-05.tar.gz                 16-Oct-2020 13:19    224M
hemiptera_odb10.2020-08-05.tar.gz                  16-Oct-2020 13:19    115M
hymenoptera_odb10.2020-08-05.tar.gz                16-Oct-2020 13:19    321M
hypocreales_odb10.2020-08-05.tar.gz                16-Oct-2020 13:19    224M
insecta_odb10.2020-09-10.tar.gz                    16-Oct-2020 13:20    119M
lactobacillales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19      9M
laurasiatheria_odb10.2020-09-10.tar.gz             16-Oct-2020 13:20    688M
legionellales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     16M
leotiomycetes_odb10.2020-08-05.tar.gz              16-Oct-2020 13:19    164M
lepidoptera_odb10.2020-08-05.tar.gz                16-Oct-2020 13:20    241M
liliopsida_odb10.2020-09-10.tar.gz                 16-Oct-2020 13:20    163M
mammalia_odb10.2020-09-10.tar.gz                   16-Oct-2020 13:19    677M
metazoa_odb10.2020-09-10.tar.gz                    16-Oct-2020 13:19    127M
methanobacteria_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     15M
methanococcales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:20     17M
methanomicrobia_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     12M
methanomicrobiales_odb10.2020-03-06.tar.gz         16-Oct-2020 13:20     16M
micrococcales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     12M
microsporidia_odb10.2020-08-05.tar.gz              16-Oct-2020 13:20     26M
mollicutes_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:20      3M
mollusca_odb10.2020-08-05.tar.gz                   16-Oct-2020 13:20    266M
mucorales_odb10.2020-08-05.tar.gz                  16-Oct-2020 13:20    105M
mucoromycota_odb10.2020-08-05.tar.gz               16-Oct-2020 13:19     75M
mycoplasmatales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19      4M
natrialbales_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     24M
neisseriales_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     16M
nematoda_odb10.2020-08-05.tar.gz                   16-Oct-2020 13:20    138M
nitrosomonadales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:19     15M
nostocales_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:19     35M
oceanospirillales_odb10.2020-03-06.tar.gz          16-Oct-2020 13:19     13M
onygenales_odb10.2020-08-05.tar.gz                 16-Oct-2020 13:19    233M
oscillatoriales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     29M
passeriformes_odb10.2020-08-05.tar.gz              16-Oct-2020 13:20    298M
pasteurellales_odb10.2020-03-06.tar.gz             16-Oct-2020 13:19     19M
planctomycetes_odb10.2020-03-06.tar.gz             16-Oct-2020 13:19     13M
plasmodium_odb10.2020-08-05.tar.gz                 16-Oct-2020 13:20    199M
pleosporales_odb10.2020-08-05.tar.gz               16-Oct-2020 13:19    288M
poales_odb10.2020-08-05.tar.gz                     16-Oct-2020 13:19    186M
polyporales_odb10.2020-08-05.tar.gz                16-Oct-2020 13:20    206M
primates_odb10.2020-08-05.tar.gz                   16-Oct-2020 13:19    451M
propionibacteriales_odb10.2020-03-06.tar.gz        16-Oct-2020 13:19     14M
proteobacteria_odb10.2020-03-06.tar.gz             16-Oct-2020 13:19      8M
pseudomonadales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     17M
rhizobiales_odb10.2020-03-06.tar.gz                16-Oct-2020 13:19     15M
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rhodobacterales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     19M
rhodospirillales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:19     14M
rickettsiales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19      8M
saccharomycetes_odb10.2020-08-05.tar.gz            16-Oct-2020 13:20    109M
sauropsida_odb10.2020-09-10.tar.gz                 16-Oct-2020 13:19    499M
selenomonadales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     16M
solanales_odb10.2020-08-05.tar.gz                  16-Oct-2020 13:19    196M
sordariomycetes_odb10.2020-08-05.tar.gz            16-Oct-2020 13:19    206M
sphingobacteriia_odb10.2020-03-06.tar.gz           16-Oct-2020 13:20     21M
sphingomonadales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:19     22M
spirochaetales_odb10.2020-03-06.tar.gz             16-Oct-2020 13:20      8M
spirochaetes_odb10.2020-03-06.tar.gz               16-Oct-2020 13:20      6M
spirochaetia_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19      6M
stramenopiles_odb10.2020-08-05.tar.gz              16-Oct-2020 13:19      5M
streptomycetales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:20     31M
streptosporangiales_odb10.2020-03-06.tar.gz        16-Oct-2020 13:19     22M
sulfolobales_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     22M
synechococcales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     16M
synergistetes_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     14M
tenericutes_odb10.2020-03-06.tar.gz                16-Oct-2020 13:20      4M
tetrapoda_odb10.2020-09-10.tar.gz                  16-Oct-2020 13:19    561M
thaumarchaeota_odb10.2020-03-06.tar.gz             16-Oct-2020 13:20     13M
thermoanaerobacterales_odb10.2020-03-06.tar.gz     16-Oct-2020 13:19     10M
thermoplasmata_odb10.2020-03-06.tar.gz             16-Oct-2020 13:20      7M
thermoproteales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19      8M
thermoprotei_odb10.2020-03-06.tar.gz               16-Oct-2020 13:20      6M
thermotogae_odb10.2020-03-06.tar.gz                16-Oct-2020 13:19     16M
thiotrichales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:20     11M
tissierellales_odb10.2020-03-06.tar.gz             16-Oct-2020 13:19      9M
tissierellia_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19      8M
tremellomycetes_odb10.2020-08-05.tar.gz            16-Oct-2020 13:19    210M
verrucomicrobia_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     11M
vertebrata_odb10.2020-09-10.tar.gz                 16-Oct-2020 13:19    409M
vibrionales_odb10.2020-03-06.tar.gz                16-Oct-2020 13:20     26M
viridiplantae_odb10.2020-09-10.tar.gz              16-Oct-2020 13:20     36M
xanthomonadales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     24M

Address of the bookmark: https://busco-data.ezlab.org/v4/data/lineages/

MGRA: Breakpoint graphs and ancestral genome reconstructions

Jit — Tue, 25 Jul 2017 08:48:25 -0500

MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and evolutionary history of extant genomes.

It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and produces such sequences for ancestral genomes at the internal nodes of the phylogenetic tree.

The phylogenetic tree may be also specified completely or partially, in the latter case MGRA can reconstruct conserved ancestral regions (CARs) of the ancestral genome of interest.

Since version 2 MGRA supports gene insertion and deletions in addition to genome rearrangements and allows the input genomes to have different gene content.

It also can reconstruct most plausible phylogenetic tree based on the rearrangement characters.

Address of the bookmark: http://mgra.cblab.org/

Genomicus: genome browser that enables users to navigate in genomes in several dimensions

Jit — Sat, 18 Nov 2017 16:10:16 -0600

Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Address of the bookmark: http://genomicus.biologie.ens.fr/genomicus-90.01/cgi-bin/search.pl

Scripts for the analysis of HGT in genome sequence data.

Jit — Wed, 29 Nov 2017 16:44:10 -0600

Scripts for the analysis of HGT in genome sequence data

Address of the bookmark: https://github.com/reubwn/hgt