PHYRN: a robust method for phylogenetic analysis of highly divergent sequences (Q34238523)

31 July 2017

PHYRN: a robust method for phylogenetic analysis of highly divergent sequences (English)

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31 July 2017

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13

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31 July 2017

Gaurav Bhardwaj

1

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31 July 2017

Kyung Dae Ko

2

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31 July 2017

Yoojin Hong

3

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31 July 2017

Zhenhai Zhang

4

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31 July 2017

Ngai Lam Ho

5

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31 July 2017

Sree V Chintapalli

6

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31 July 2017

Lindsay A Kline

7

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31 July 2017

Matthew Gotlin

8

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31 July 2017

David Nicholas Hartranft

9

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31 July 2017

Morgen E Patterson

10

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31 July 2017

Foram Dave

11

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31 July 2017

Evan J Smith

12

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31 July 2017

Randen L Patterson

14

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31 July 2017

Damian B van Rossum

15

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31 July 2017

language of work or name

English

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publication date

13 April 2012

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31 July 2017

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31 July 2017

7

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31 July 2017

4

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31 July 2017

e34261

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Creative Commons CC0 License

31 July 2017

start time

13 April 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

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cites work

Predicting protein folds with fold-specific PSSM libraries

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Conserved GXXXG- and S/T-like motifs in the transmembrane domains of NS4B protein are required for hepatitis C virus replication

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Multiple sequence alignment: a major challenge to large-scale phylogenetics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

CDD: a Conserved Domain Database for the functional annotation of proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Death-associated protein kinase-mediated cell death modulated by interaction with DANGER

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Cnidarians and the evolutionary origin of the nervous system

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Multiple alignment of DNA sequences with MAFFT

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

FastTree: computing large minimum evolution trees with profiles instead of a distance matrix

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

An improved general amino acid replacement matrix

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Is multiple-sequence alignment required for accurate inference of phylogeny?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Ancient origin of the new developmental superfamily DANGER

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Probalign: multiple sequence alignment using partition function posterior probabilities

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

The average common substring approach to phylogenomic reconstruction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

An algorithm for progressive multiple alignment of sequences with insertions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Scoredist: a simple and robust protein sequence distance estimator

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

MUSCLE: multiple sequence alignment with high accuracy and high throughput

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

MrBayes 3: Bayesian phylogenetic inference under mixed models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Expression of zebrafish mab21 genes marks the differentiating eye, midbrain and neural tube

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Pairwise sequence alignment below the twilight zone

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Profile hidden Markov models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Rose: generating sequence families.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

The mab-21 gene of Caenorhabditis elegans encodes a novel protein required for choice of alternate cell fates.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Toward extracting all phylogenetic information from matrices of evolutionary distances

6 July 2018

1 reference

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A review of long-branch attraction

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0034261

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0034261

Inferring evolutionary trees with PAUP*.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0034261

Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0034261

DANGER, a novel regulatory protein of inositol 1,4,5-trisphosphate-receptor activity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0034261

Anandamide and arachidonic acid use epoxyeicosatrienoic acids to activate TRPV4 channels

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0034261

A comparison of MSA tools

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0034261

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0034261

Within the twilight zone: a sensitive profile-profile comparison tool based on information theory.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

Embryonic XMab21l2 expression is required for gastrulation and subsequent neural development.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325999

A simulation test bed for hypotheses of genome evolution

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22514627

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0034261

1 reference

31 July 2017

0 references

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31 July 2017

1 reference