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Literature DB >> 21527926

PhymmBL expanded: confidence scores, custom databases, parallelization and more.

Arthur Brady, Steven Salzberg.

Abstract

Entities: Species

Mesh：

Year: 2011 PMID： 21527926 PMCID： PMC3319356 DOI： 10.1038/nmeth0511-367

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

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3 in total

1. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.

Authors: Hendrik N Poinar; Carsten Schwarz; Ji Qi; Beth Shapiro; Ross D E Macphee; Bernard Buigues; Alexei Tikhonov; Daniel H Huson; Lynn P Tomsho; Alexander Auch; Markus Rampp; Webb Miller; Stephan C Schuster
Journal: Science Date: 2005-12-20 Impact factor: 47.728

Review 2. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors: S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal: Nucleic Acids Res Date: 1997-09-01 Impact factor: 16.971

3. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.

Authors: Arthur Brady; Steven L Salzberg
Journal: Nat Methods Date: 2009-08-02 Impact factor: 28.547

3 in total

62 in total

Review 1. Molecular phylogenetics: principles and practice.

Authors: Ziheng Yang; Bruce Rannala
Journal: Nat Rev Genet Date: 2012-03-28 Impact factor: 53.242

Review 2. Application of computational methods in genetic study of inflammatory bowel disease.

Authors: Jin Li; Zhi Wei; Hakon Hakonarson
Journal: World J Gastroenterol Date: 2016-01-21 Impact factor: 5.742

3. Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community.

Authors: Sheila Podell; Joanne B Emerson; Claudia M Jones; Juan A Ugalde; Sue Welch; Karla B Heidelberg; Jillian F Banfield; Eric E Allen
Journal: ISME J Date: 2013-12-12 Impact factor: 10.302

4. Census-based rapid and accurate metagenome taxonomic profiling.

Authors: Amirhossein Shamsaddini; Yang Pan; W Evan Johnson; Konstantinos Krampis; Mariya Shcheglovitova; Vahan Simonyan; Amy Zanne; Raja Mazumder
Journal: BMC Genomics Date: 2014-10-21 Impact factor: 3.969

5. TIPP: taxonomic identification and phylogenetic profiling.

Authors: Nam-Phuong Nguyen; Siavash Mirarab; Bo Liu; Mihai Pop; Tandy Warnow
Journal: Bioinformatics Date: 2014-10-29 Impact factor: 6.937

Review 6. Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics.

Authors: Anukriti Sharma; Rup Lal
Journal: Indian J Microbiol Date: 2016-11-11 Impact factor: 2.461

7. New approach for phylogenetic tree recovery based on genome-scale metabolic networks.

Authors: Daniel Gamermann; Arnaud Montagud; J Alberto Conejero; Javier F Urchueguía; Pedro Fernández de Córdoba
Journal: J Comput Biol Date: 2014-03-10 Impact factor: 1.479

8. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.

Authors: Todd J Treangen; Sergey Koren; Daniel D Sommer; Bo Liu; Irina Astrovskaya; Brian Ondov; Aaron E Darling; Adam M Phillippy; Mihai Pop
Journal: Genome Biol Date: 2013-01-15 Impact factor: 13.583

Review 9. Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.

Authors: Eric A Franzosa; Tiffany Hsu; Alexandra Sirota-Madi; Afrah Shafquat; Galeb Abu-Ali; Xochitl C Morgan; Curtis Huttenhower
Journal: Nat Rev Microbiol Date: 2015-04-27 Impact factor: 60.633

Review 10. Ancient and modern environmental DNA.

Authors: Mikkel Winther Pedersen; Søren Overballe-Petersen; Luca Ermini; Clio Der Sarkissian; James Haile; Micaela Hellstrom; Johan Spens; Philip Francis Thomsen; Kristine Bohmann; Enrico Cappellini; Ida Bærholm Schnell; Nathan A Wales; Christian Carøe; Paula F Campos; Astrid M Z Schmidt; M Thomas P Gilbert; Anders J Hansen; Ludovic Orlando; Eske Willerslev
Journal: Philos Trans R Soc Lond B Biol Sci Date: 2015-01-19 Impact factor: 6.237