Address of the bookmark: https://github.com/DessimozLab/OMArk

Address of the bookmark: http://www.compbio.dundee.ac.uk/jpred4/

[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

We developed a novel, self-contained technique named Near HGT, based on the synteny index, to measure the divergence of a gene from its native genomic environment and used it to identify candidate HGT events between closely related strains. The method confirms candidate transferred genes based on the constant relative mutability (CRM). Using CRM, the algorithm assigns a confidence score based on “unusual” sequence divergence. A gene exhibiting exceptional deviations according to both synteny and mutability criteria, is considered a validated HGT product. We first employed the technique to a set of three E. coli strains and detected several highly probable horizontally acquired genes. We then compared the method to existing HGT detection tools using a larger strain data set.

When combined with additional approaches our new algorithm provides richer picture and brings us closer to the goal of detecting all newly acquired genes in a particular strain.

Availability: The method is publicly available athttp://research.haifa.ac.il/~ssagi/software/nearHGT.zip

Address of the bookmark: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004408

Address of the bookmark: https://github.com/mkirsche/Jasmine

Following are the popular tool to detect HGT in genomes:

T-REX / 3.22

HGT detection / download & compile

20525630

RANGER-DTL / 2.0

HGT detection / download binary

22689773

PhyloNet / 3.6.1

HGT detection / download binary

18662388

Jane / 4.01

HGT detection / download binary (!license!)

20181081

TREE-PUZZLE / 5.3.rc16

HGT detection / download & compile

11934758

CONSEL / 0.20

HGT detection / download

11751242

DarkHorse / 1.5 rev170

HGT detection / download & install

17274820

HGTector / 0.2.1

HGT detection / git clone

25159222

EGID / 1.0

HGT detection / download

22355228

GeneMarkS / 4.30

HGT detection / download binary (!license!)

9461475

##################################################
[Mon May 7 11:29:18 2018] Reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
test/run1/contigs.fa 163897 245 66377 40.50 221 90.20 94.854 0 97520 59.50 24 9.80

##################################################
[Mon May 7 11:29:29 2018] Estimating parameters of libraries...
Aligning 19504 mates per library...
Insert size statistics Mates orientation stats
FastQ files read length median mean stdev FF FR RF RR
test/5000_1.fq.gz test/5000_2.fq.gz 50 4998 4990.20 721.47 0 4674 0 0
test/600_1.fq.gz test/600_2.fq.gz 100 599 598.63 47.68 0 10000 0 0

##################################################
[Mon May 7 11:29:29 2018] Scaffolding...
iteration 1.1: test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
19505 pairs. 17302 passed filtering [88.71%]. 1627 in different contigs [8.34%].
1526 pairs. 558 in different contigs [36.57%].
iteration 1.2: test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 17607 passed filtering [90.27%]. 182 in different contigs [0.93%].
1077 pairs. 124 in different contigs [11.51%].
iteration 2.1: test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 15112 passed filtering [77.48%]. 1295 in different contigs [6.64%].
3417 pairs. 396 in different contigs [11.59%].
iteration 2.2: test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
19505 pairs. 15152 passed filtering [77.68%]. 0 in different contigs [0.00%].
3398 pairs. 0 in different contigs [0.00%].

##################################################
[Mon May 7 11:29:34 2018] Gap closing...
iteration 1.1: test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133

##################################################
[Mon May 7 11:29:35 2018] Final reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
[WARNING] Nothing reduced!
test/run1/scaffolds.filled.fa 99390 1 0 0.00 0 0.00 0.000 0 99390 100.00 1 100.00

##################################################
[Mon May 7 11:29:35 2018] Reporting statistics...
#fname contigs bases GC [%] contigs >1kb bases in contigs >1kb N50 N90 Ns longest
test/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_sspace.2.2.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_gapcloser.1.1.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.filled.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.reduced.fa 1 99390 39.689 1 99390 99390 99390 2 99390

##################################################
[Mon May 7 11:29:35 2018] Cleaning-up...
#Time elapsed: 0:00:17.376924

Address of the bookmark: https://github.com/knausb/vcfR

ashr - https://github.com/stephens999/ashr, https://cran.r-project.org/web/packages/ashr/index.html

consensusDE - https://bioconductor.org/packages/release/bioc/html/consensusDE.html

DESeq2 - https://bioconductor.org/packages/release/bioc/html/DESeq2.html

edgeR - https://bioconductor.org/packages/release/bioc/html/edgeR.html

limma - https://kasperdanielhansen.github.io/genbioconductor/html/limma.html  https://bioconductor.org/packages/release/bioc/html/limma.html

MetaCycle - https://cran.r-project.org/web/packages/MetaCycle/index.html, https://github.com/gangwug/MetaCycle

RUVSeq - https://bioconductor.org/packages/release/bioc/html/RUVSeq.html

SARTools - https://github.com/PF2-pasteur-fr/SARTools

tximport - https://github.com/mikelove/tximport

Applications are invited for a post in DST, India funded Project entitled: "Positive and negative impacts of macromolecular crowding agents during target site location by DNA binding proteins – origin of optimal search at physiological ionic concentration (Reference Number: ECR/2016/000188) ''. The selected candidate will be appointed purely on temporary basis, initially for two years as a JRF that may be extended to one year of SRF based on the performance.

Position: Junior Research Fellow (1)

Qualifications & Experience: Candidate must have a consistently good academic record with at least 60% marks in all throughout and must have qualified NET/GATE.

Desirable: Basic knowledge in the field of biophysics, molecular simulations and computational biology are desirable.

Salary: Consolidated Rs. 25,000 per month.

Tenure: The project duration is for three years and the selected candidate would be appointed after an interview. Appointment will be purely on temporary basis as stipulated by the existing rules of the University.

Interested candidates need to send an application to the address mentioned below mentioning the name of the project and post applied for (on the cover of the envelope).

The applications along with CV should be mailed at the address given below. Name, address, contact number and e. mail address of two referees must be enclosed with the application. The last date for the application is July 31st 2016.

Dr. Arnab Bhattacharjee (Principal Investigator)
Assistant Professor
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi-110067
E-mail: arnab@jnu.ac.in

Note: 1. Only shortlisted candidates will be communicated to appear in the interview at SCIS, JNU and no other communications in this regard will be entertained.

2. No TA/DA will be paid for appearing in interview.