(Q21145358)

17 August 2022

Ian Holmes

Ian

Holmes

1 reference

17 August 2022

Robert K Bradley

Robert K

Bradley

1 reference

17 August 2022

Colin Dewey

Colin

Dewey

1 reference

17 August 2022

Michael Smoot

Michael

Smoot

1 reference

17 August 2022

Adam Roberts

Adam

Roberts

1 reference

17 August 2022

Sudeep Juvekar

series ordinal

author given names

Sudeep

author last names

Juvekar

1 reference

17 August 2022

Jaeyoung Do

Jaeyoung

1 reference

PLOS Computational Biology

17 August 2022

language of work or name

English

0 references

publication date

May 2009

0 references

published in

0 references

volume

0 references

issue

0 references

page(s)

e1000392

0 references

Creative Commons Attribution 4.0 International

start time

29 May 2009

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

describes a project that uses

MUMmer

object named as

MUMmer

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

An enhanced RNA alignment benchmark for sequence alignment programs

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Automated generation of heuristics for biological sequence comparison

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

ProbCons: Probabilistic consistency-based multiple sequence alignment

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Rfam: annotating non-coding RNAs in complete genomes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Indel-based evolutionary distance and mouse-human divergence

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Versatile and open software for comparing large genomes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

The European ribosomal RNA database

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Evolution of genes and genomes on the Drosophila phylogeny

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Clustal W and Clustal X version 2.0

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

The Jalview Java alignment editor

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

T-Coffee: A novel method for fast and accurate multiple sequence alignment

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Comprehensive study on iterative algorithms of multiple sequence alignment

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Recent developments in the MAFFT multiple sequence alignment program

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Aligning multiple genomic sequences with the threaded blockset aligner

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Multiple sequence alignment using partial order graphs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Probabilistic phylogenetic inference with insertions and deletions

10 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Segment-based multiple sequence alignment

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

HMMoC--a compiler for hidden Markov models

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Multiple sequence alignment.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

MAVID: constrained ancestral alignment of multiple sequences

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Comparison of genomic DNA sequences: solved and unsolved problems

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Dynamic programming alignment accuracy

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Multiple DNA and protein sequence alignment based on segment-to-segment comparison

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Alignment uncertainty and genomic analysis

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Probalign: multiple sequence alignment using partition function posterior probabilities

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Specific alignment of structured RNA: stochastic grammars and sequence annealing

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Uncertainty in homology inferences: assessing and improving genomic sequence alignment

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Transducers: an emerging probabilistic framework for modeling indels on trees

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Multiple alignment by sequence annealing.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

DNA assembly with gaps (Dawg): simulating sequence evolution

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

An algorithm for statistical alignment of sequences related by a binary tree.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Statistical alignment: computational properties, homology testing and goodness-of-fit.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

TEXshade: shading and labeling of multiple sequence alignments using LATEX2 epsilon.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2684580

Using guide trees to construct multiple-sequence evolutionary HMMs

29 November 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/19478997

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark

1 reference

https://pubmed.ncbi.nlm.nih.gov/19478997

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

SABmark--a benchmark for sequence alignment that covers the entire known fold space

1 reference

https://pubmed.ncbi.nlm.nih.gov/19478997

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1000392

1 reference

journals/ploscb/BradleyRSJDDHP09

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

1 reference

1 reference