Alignathon: a competitive assessment of whole-genome alignment methods

TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction

(2014) Jia-Ming Chang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Decoding long nanopore sequencing reads of natural DNA

(2014) Andrew H Laszlo et al.   NATURE BIOTECHNOLOGY

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

(2013) Carsten Kemena et al.   BIOINFORMATICS

PSAR-Align: improving multiple sequence alignment using probabilistic sampling

(2013) J. Kim et al.   BIOINFORMATICS

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

(2013)   JOURNAL OF HEREDITY

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

(2013) J. Schreiber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Keith R Bradnam et al.   GigaScience

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Avinash Varadarajan et al.   GENOME BIOLOGY

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

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

(2011) D. Earl et al.   GENOME RESEARCH

ALF—A Simulation Framework for Genome Evolution

(2011) Daniel A. Dalquen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Kerstin Lindblad-Toh et al.   NATURE

PSAR: measuring multiple sequence alignment reliability by probabilistic sampling

(2011) Jaebum Kim et al.   NUCLEIC ACIDS RESEARCH

Mugsy: fast multiple alignment of closely related whole genomes

(2010) Samuel V. Angiuoli et al.   BIOINFORMATICS

An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty

(2010) O. Penn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative assessment of methods for aligning multiple genome sequences

(2010) Xiaoyu Chen et al.   NATURE BIOTECHNOLOGY

GUIDANCE: a web server for assessing alignment confidence scores

(2010) O. Penn et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

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

(2009) Carsten Kemena et al.   BIOINFORMATICS

Simulation of Genes and Genomes Forward in Time

(2009) Antonio Carvajal-Rodriguez   CURRENT GENOMICS

Multiple whole-genome alignments without a reference organism

(2009) I. Dubchak et al.   GENOME RESEARCH

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

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

(2008) Benedict Paten et al.   BIOINFORMATICS

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

(2008) B. Paten et al.   GENOME RESEARCH

Genome size diversity in the family Drosophilidae

(2008) T R Gregory et al.   HEREDITY

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE