Address of the bookmark: https://breedbase.org/

Furthermore, it displays the tree in a mobile phone (iPhone and Android) if the input file size is small.  CITATION: Subramanian, S., Ramasamy, U. and Chen, D. (2019).  VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs.  Peer J. x:yy.

Address of the bookmark: https://github.com/sansubs/vcf2pop

More at http://www.cmdn.org.np/main/index.php

dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. 

Address of the bookmark: https://github.com/lijuzeng/dna2bit

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

CSIR-IICT is conducting Walk in Interview for the following position on a purely temporary basis for the sponsored project "GENESIS (BSC-0121) at 10.00 AM on 19th August 2014 at IICT, Hyderabad

Position : Research Associate
No of Post : One
Desired Profile : PhD in computation biology or M.Tech in Computational Biology with three years experience in relevant subject and atleast one research paper in SCI journal

Experience : Knowledge in vector and vector borne disease, disease modeling, GIS mapping and modeling.
Age : 35 years
Stipend : Rs 22000/- + HRA

Eligible candidate may download the application form from our website http://www.iictindia.org and appear for interview along with the duly filled in application form supported by bio-data and one set of attested photo copies of certificates of educational qualification, age, experience, caste, latest photograph and the cadndidates are required to bring all the original certificates for verification

Walk in Interview : 19.08.14

##################################################
[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

Applications are invited for the post of Junior Research Fellow (JRF) in a DBT funded IYBA project entitled “Generatingaprotein-ncRNA interactome for Dorsal mediated gene regulation and dorso-ventral patterning genes in Drosophila” in the Lab. Of Molecular Biology at the Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi. The project requires extensive use of molecular, genetic and genomic approaches.

POST: Junior Research Fellow (JRF)

NO. OF VACANCIE(S) - (01)

FELLOWSHIP: Rs. 16,000/- plus HRA

PROJECT DURATION: 2014-2016 (Two years)

LAST DATE FOR APPLICATION: Aug 18, 2014.

Eligibility criteria:

M.Sc./M.Tech./ in Biological Sciences/Biotechnology/Bio-Informatics. Candidates with research experience in the field of Drosophila/Yeast genetics will be preferred.

Application Procedure:

A covering letter along with your CV, copy of prior publications (if any) and proof of experience should be e-mailed to lmb_sau@aol.com. Hardcopy of the application should be brought on the day of interview along with other testimonials and marks statements for verification purpose.

IMPORTANT NOTE:

-No TA/DA will be paid for attending the interview.

-SAU may select candidates against the post depending upon qualification and experience of candidates and reserves the right to relax any of the qualifications in case the candidate is found otherwise well qualified by the Selection Committee

-The abovementioned post is temporary and will be initially offered for a period of one year and can be extended, on satisfactory performance.

More at http://www.sau.ac.in/recruitment/vacancy.html