BOL: Related items

Charpak exchange program

Fri, 10 Nov 2023 02:33:38 -0600

The scholarship is designed for Indian students from all fields and streams of study, enrolled in an Indian institution at the Bachelors or Master’s degree level, who wish to undertake a study exchange semester programme in France (for a period of one to six months).

BENEFITS
The Charpak exchange program offers the following benefits to the awardees based on merit: monthly stipend of 860 euros social security student visa and Campus France fee waiver assistance in finding an affordable student accommodation (subject to availability)

https://www.inde.campusfrance.org/charpak-exchange-scholarship-spring-session-jan-june

MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times

Poonam Mahapatra — Sat, 02 Jun 2018 07:40:06 -0500

MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of the PAML package. In this tutorial I will analyze an easy example modified from dataset of Inoue et al. (2010). Here we conduct a commonly used time estimation method, "Approximate Likelihood Method", for the datasets including more than 10 species.

Address of the bookmark: http://www.fish-evol.com/mcmctreeExampleVert6/text1Eng.html

DISTRUCT: a program for the graphical display of population structure

Abhimanyu Singh — Mon, 25 Mar 2019 03:33:44 -0500

distruct is a program that can be used to graphically display results produced by the genetic clustering program structure or by other similar programs. The figures produced by distructdisplay individual membership coefficients in the same form as used in "Genetic structure of human populations" Science 298: 2381-2385 (2002). Various options enable the user to control left-to-right printing order of populations, bottom-to-top printing order of clusers, colors, and other graphical details. [Example]

[Download software package (includes the manual)] (you will be directed first to a registration page and we would very much appreciate if you register)
[Download manual]
[Download software note from Molecular Ecology Notes 4: 137-138 (2004)]

To use the UNIX versions, unzip and untar the files in an appropriate directory using

gunzip filename.tar.gz; tar xvf filename.tar

where "filename.tar.gz" is the downloaded file. Winzip will unzip the Windows version. Run the program by typing

./distruct

in UNIX or

distruct

from a Dos prompt in Windows. It will produce a figure using the data that are represented in the Central/South Asia K=5 plot in Science 298: 2381-2385 (2002).

Please send comments or problems with distruct to Noah Rosenberg.

October 15, 2014 — Users of Distruct may also find CLUMPP and CLUMPAK of interest.

Address of the bookmark: https://rosenberglab.stanford.edu/distruct.html

chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

Jit — Mon, 23 Mar 2020 06:20:04 -0500

Python package to detect chromatin loops (and other patterns) in Hi-C contact maps.

Stable version with pip:

pip3 install --user chromosight

Stable version with conda:

conda install -c bioconda -c conda-forge chromosight

or, if you want to get the latest development version:

pip3 install --user -e git+https://github.com/koszullab/chromosight.git@master#egg=chromosight

Address of the bookmark: https://github.com/koszullab/Chromosight