(Q34590504)

3 August 2017

Alignathon: a competitive assessment of whole-genome alignment methods (English)

1 reference

3 August 2017

whole genome sequencing

1 reference

13

1 reference

3 August 2017

17

1 reference

3 August 2017

19

1 reference

3 August 2017

25

David Haussler

0 references

Ionas Erb

14

0 references

Aaron Earl Darling

20

0 references

Cedric Notredame

22

Cedric Notredame

0 references

Carsten Kemena

Carsten Kemena

12

0 references

Benedict Paten

26

Benedict Paten

1 reference

3 August 2017

10

Hiram Clawson

1 reference

3 August 2017

23

Michael Brudno

1 reference

3 August 2017

Jian Ma

21

0 references

Brian J Raney

9

Brian J Raney

1 reference

3 August 2017

24

Inna Dubchak

1 reference

3 August 2017

Dent Earl

1

1 reference

3 August 2017

Ngan Nguyen

2

1 reference

3 August 2017

Glenn Hickey

3

1 reference

3 August 2017

Robert S Harris

4

1 reference

3 August 2017

Stephen Fitzgerald

5

1 reference

3 August 2017

Kathryn Beal

6

1 reference

3 August 2017

Igor Seledtsov

7

1 reference

3 August 2017

Vladimir Molodtsov

8

1 reference

3 August 2017

Jaebum Kim

11

1 reference

3 August 2017

Alexander Poliakov

15

1 reference

3 August 2017

Minmei Hou

16

1 reference

3 August 2017

William James Kent

18

1 reference

3 August 2017

1 October 2014

1 reference

3 August 2017

1 reference

3 August 2017

24

1 reference

3 August 2017

2077-2089

1 reference

3 August 2017

12

1 reference

Decoding long nanopore sequencing reads of natural DNA

3 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

PSAR-align: improving multiple sequence alignment using probabilistic sampling.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

The UCSC Genome Browser database: extensions and updates 2013.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

An integrated encyclopedia of DNA elements in the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

ALF--a simulation framework for genome evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

A high-resolution map of human evolutionary constraint using 29 mammals

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Assemblathon 1: a competitive assessment of de novo short read assembly methods

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Cactus: Algorithms for genome multiple sequence alignment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

PSAR: measuring multiple sequence alignment reliability by probabilistic sampling.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Identification of functional elements and regulatory circuits by Drosophila modENCODE

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Mugsy: fast multiple alignment of closely related whole genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

The UCSC Genome Browser database: update 2011

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Simulation of genes and genomes forward in time

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

GUIDANCE: a web server for assessing alignment confidence scores.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

An alignment confidence score capturing robustness to guide tree uncertainty

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Fast statistical alignment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Multiple whole-genome alignments without a reference organism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

The potential and challenges of nanopore sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

LOCAL RELIABILITY MEASURES FROM SETS OF CO-OPTIMAL MULTIPLE SEQUENCE ALIGNMENTS

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Alignment uncertainty and genomic analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Evolution of genes and genomes on the Drosophila phylogeny

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

28-way vertebrate alignment and conservation track in the UCSC Genome Browser

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Recent evolutions of multiple sequence alignment algorithms

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

An enhanced RNA alignment benchmark for sequence alignment programs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

TimeTree: a public knowledge-base of divergence times among organisms

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Multiple sequence alignment.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Multiple sequence alignments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Mauve: multiple alignment of conserved genomic sequence with rearrangements

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

VISTA: computational tools for comparative genomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Aligning multiple genomic sequences with the threaded blockset aligner

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Sequencing and comparison of yeast species to identify genes and regulatory elements

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Tandem repeats finder: a program to analyze DNA sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Dynamic programming alignment accuracy

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

DNA assembly with gaps (Dawg): simulating sequence evolution.

7 July 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.174920.114

Comparative assessment of methods for aligning multiple genome sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.174920.114

Aligning multiple whole genomes with Mercator and MAVID.

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.174920.114

FusionDB: a database for in-depth analysis of prokaryotic gene fusion events

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.174920.114

Genome size diversity in the family Drosophilidae

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.174920.114

Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package.

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.174920.114

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.174920.114

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.174920.114

Analysis and comparison of benchmarks for multiple sequence alignment

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248324

A simulation test bed for hypotheses of genome evolution

27 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25273068

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.174920.114

1 reference

3 August 2017

1 reference

3 August 2017

1 reference