A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants

Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize

(2021) Baoxing Song et al.   GENOME RESEARCH

K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes

(2021) Bruno Contreras‐Moreira et al.   Plant Genome

GSAlign: an efficient sequence alignment tool for intra-species genomes

(2020) Hsin-Nan Lin et al.   BMC GENOMICS

Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ

(2020) Ilia Minkin et al.   Nature Communications

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

The maize W22 genome provides a foundation for functional genomics and transposon biology

(2018) Nathan M. Springer et al.   NATURE GENETICS

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

(2018) Silong Sun et al.   NATURE GENETICS

Whole-Genome Alignment and Comparative Annotation

(2018) Joel Armstrong et al.   Annual Review of Animal Biosciences

A review on multiple sequence alignment from the perspective of genetic algorithm

(2017) Biswanath Chowdhury et al.   GENOMICS

Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation

(2017) Virag Sharma et al.   NUCLEIC ACIDS RESEARCH

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale

(2015) Hani Z. Girgis   BMC BIOINFORMATICS

Resolving deep relationships of PACMAD grasses: a phylogenomic approach

(2015) Joseph L. Cotton et al.   BMC PLANT BIOLOGY

Split-alignment of genomes finds orthologies more accurately

(2015) Martin C Frith et al.   GENOME BIOLOGY

Improved search heuristics find 20 000 new alignments between human and mouse genomes

(2014) Martin C. Frith et al.   NUCLEIC ACIDS RESEARCH

Molecular Dating, Evolutionary Rates, and the Age of the Grasses

(2013) P.-A. Christin et al.   SYSTEMATIC BIOLOGY

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH