BOL: Related items

Genomic Basis of Evolutionary Innovations (GEvol)

BioStar — Sat, 06 Dec 2025 06:11:00 -0600

The Priority Programme (SPP 2349) funded by German Science Foundation (DFG) started 2022: „Genomic Basis of Evolutionary Innovations (GEvol)“

GEvol is unique as it will use, for the first time, a large taxonomic group to focus on one goal: to characterise the dynamics and mechanisms of genomic innovations underlying novel traits using comparative evolutionary genomics (and related data).
Thus, projects participating in GEvol we will ask fundamental evolutionary questions such as:
1. At what level is evolution repeatable?
2. How does genomic plasticity interfere with phenotypic plasticity during evolution?
3. How do inter- and intra-specific interactions influence genomic architectures?
4. How predictable is phenotypic variation given some knowledge about the dynamics and mechanisms of underlying genome evolution?

Address of the bookmark: https://g-evol.uni-muenster.de/open-positions/

Hejnol Group

Thu, 22 Feb 2018 16:02:53 -0600

The group studies a broad range of animal taxa using morphological and molecular tools to unravel the evolution and development of animal organ systems.

To understand the evolution of the biodiversity seen on planet earth is one of the major goals in biology. How animals explored new habitats from only being confined to the marine environment and the how the forms diversified is still one of the most tremendous questions to be answered.

http://www.sars.no/research/HejnolGrp.php

Gupta Lab

Sat, 29 Dec 2018 13:18:31 -0600

Work include (i) understanding the evolutionary relationships among different prokaryotic and eukaryotic organisms; (ii) Understanding the cellular functions of these lineage-specific signature proteins as well as lineage-specific conserved inserts and deletions in important housekeeping proteins by genetic and biochemical studies; (iii) Development of novel diagnostic methods (PCR based and immunological) for identification of different groups of organisms based upon these signature proteins and conserved indels; (iv) The use of these lineage-specific probes with predicitive ability to identify/explore the presence of different groups of organisms in metagenomic sequences from various environments.

https://fhs.mcmaster.ca/gupta-lab/index.html

TMRCA Calculator

BioStar — Wed, 03 Feb 2021 05:07:30 -0600

This program calculates the probability that two people have a certain number of generations between them, based on the standard infinite alleles formula of Walsh. It calculates both the probability of being at an exact number of generations back to the Most Recent Common Ancestor (MRCA) of a certain pair of people and the cumulative probability that the actual number of generations is less than a certain value. Note that the convention using generations is changed from an earlier version of this calculator which used "transmission events". It can list both result types in a table or graph. In either case the horizontal axis stops at the point where the cumulative probability reaches 95% or 10 generations, whichever is longer, or an absolute max of 50,000. Beyond 90% the calculation becomes inaccurate.

https://clandonaldusa.org/index.php/tmrca-calculator

Address of the bookmark: https://clandonaldusa.org/index.php/tmrca-calculator

Useful link to teach evolution !

Abhi — Wed, 05 Oct 2022 18:29:30 -0500

Mimicry and other resources
Mimicry games:
Great Heliconius game:
http://heliconius.org/evolving_butterflies/
(See also 
https://royalsocietypublishing.org/doi/10.1098/rspb.2020.0014)
Other one, a bit less friendly:
https://ccl.northwestern.edu/netlogo/models/Mimicry
Camouflage practical
https://alexis-catherine.github.io/publication/natural-selection-and-camouflage/
(NetLogo also has one: 
https://ccl.northwestern.edu/netlogo/models/BugHuntCamouflage)
Peppered moth game:
https://askabiologist.asu.edu/peppered-moths-game/play.html

General resources
The always popular Populus:
https://cbs.umn.edu/populus/overview
Drift & Gene Flow 
https://cartwrig.ht/apps/genie/
(Cock van Oosterhout has a great ppt to lead students through this)
See also https://cartwrig.ht/apps/redlynx/
https://demonstrations.wolfram.com/ReplicatorMutatorDynamicsWithThreeStrategies/
NetLogo:
http://ccl.northwestern.edu/netlogo/models/index.cgi
Population Genetics:
https://www.radford.edu/~rsheehy/Gen_flash/popgen/
Evolution in general
https://evolution.berkeley.edu/evolibrary/home.php
Mitochondrial Eve:
https://projects.ncsu.edu/cals/gn/ex/mit-eve.html
Y chromosomes:
https://projects.ncsu.edu/cals/gn/ex/y-chrom.html
A professional online package from Michael Kasumovic:
https://arludo.com/
a compilation of resources:
https://planted.botany.org/index.php?P=Home
Finally, Donald Forsdyke has some great on-line videos explaining
evolutionary principles (occasionally in a fake Scottish accent):
http://post.queensu.ca/~forsdyke/videolectures.htm

New born babies get ready to know their whole genome soon!!!

Rahul Agarwal — Thu, 05 Sep 2013 07:24:02 -0500

USA launch a pilot projects to examine medical information of newborn baby, which are being funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) and the National Human Genome Research Institute (NHGRI), both parts of the National Institutes of Health.

Awards of $5 million to four grantees have been made in fiscal year 2013 under the Genomic Sequencing and Newborn Screening Disorders research program. The program will be funded at $25 million over five years, as funds are made available.

"Hundreds of US babies will be pioneers in genomic medicine through a US$25-million programme to sequence their genomes soon after they are born."

Source:

http://blogs.nature.com/news/2013/09/scientists-to-sequence-hundreds-of-newborns-genomes.html

http://www.genome.gov/27554919

GOLD:Genomes Online Database

Jit — Wed, 26 Jul 2017 07:49:29 -0500

GOLD:Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.

https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

coursera genome assembly tutorial

Jit — Sat, 25 Nov 2017 08:57:25 -0600

Solutions to Coursera Genome Sequencing (Bioinformatics II)

Address of the bookmark: https://github.com/iansealy/coursera-assembly

Bandage: interactive visualization of de novo genome assemblies

Shruti Paniwala — Mon, 04 Dec 2017 10:09:37 -0600

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequences. BLAST searches can be performed within the Bandage graphical user interface and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analyzing de novo assemblies that are not possible through investigation of contigs alone.

Availability and implementation: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows. A full feature list and screenshots are available at http://rrwick.github.io/Bandage.

Address of the bookmark: http://rrwick.github.io/Bandage/

Mugsy: multiple whole genome alignment tool

Jit — Fri, 08 Dec 2017 17:41:14 -0600

Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.

To cite Mugsy, use:

Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes.Bioinformatics 2011 27(3):334-4

Address of the bookmark: http://mugsy.sourceforge.net/