Multiple sequence alignment

I started actively working on phylogenetic networks more than 10 years ago, when I gave a talk at the Phylogenetic Combinatorics and Applications meeting in Uppsala in July 2004.

However, before I started working on networks I had for several years been working on multiple sequence alignment methodology, and I still do. This work is also of direct relevance to network construction, of course, since faulty alignments will generate conflicting signals that can confound the biological signals that alone should appear in the network.

This year marks the 20th anniversary of my first publication in the alignment field (see the list appended below). To celebrate this I have some review / commentary articles planned. The first of these has now appeared online, and I would like to draw it to your attention:

• Morrison DA (2015) Is multiple sequence alignment an art or a science? Systematic Botany 40: 14-26.

This paper relates current sequence alignment procedures to homology assessments as they are practiced for other data. Most algorithms can be seen as implementing only one of the several criteria that are used to identify homologies, which is inadequate. Suggestions are made for improving this situation.

Note: the second of these papers has now also appeared.

There will also be a couple of upcoming blog posts canvassing a few issues that I see as important for the future development of alignment methods.

Previous Publications

Theory

Ellis J, Morrison DA (1995) Effects of sequence alignment on the phylogeny of Sarcocystis deduced from 18S rDNA sequences. Parasitology Research 81: 696-699.

Morrison DA, Ellis JT (1997) Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of Apicomplexa. Molecular Biology and Evolution 14: 428-441. [This has been the most cited of these publications, surprising me by still getting cited about once per month]

Morrison DA (2006) Multiple sequence alignment for phylogenetic purposes. Australian Systematic Botany 19: 479-539.

Morrison DA (2009) A framework for phylogenetic sequence alignment. Plant Systematics and Evolution 282: 127-149. [This was actually accepted for publication in 2007]

Morrison DA (2009) Why would phylogeneticists ignore computerized sequence alignment? Systematic Biology 58: 150-158.

Morrison DA (2010) [Book review of] ‘Sequence Alignment: Methods, Models, Concepts, and Strategies’. Systematic Biology 59: 363-365.

Empirical examples

Mugridge NB, Morrison DA, Johnson AM, Luton K, Dubey JP, Votypka J, Tenter AM (1999) Phylogenetic relationships of the genus Frenkelia: a review of its history and new knowledge gained from comparison of large subunit ribosomal RNA gene sequences. International Journal for Parasitology 29: 957-972.

Mugridge NB, Morrison DA, Heckeroth AR, Johnson AM, Tenter AM (1999) Phylogenetic analysis based on full-length large subunit ribosomal RNA gene sequence comparison reveals that Neospora caninum is more closely related to Hammondia heydorni than to Toxoplasma gondii. International Journal for Parasitology 29: 1545-1556.

Mugridge NB, Morrison DA, Jäkel T, Heckeroth AR, Tenter AM, Johnson AM (2000) Effects of sequence alignment and structural domains of ribosomal DNA on phylogeny reconstruction for the protozoan family Sarcocystidae. Molecular Biology and Evolution 17: 1842-1853.

Beebe NW, Cooper RD, Morrison DA, Ellis JT (2000) Subset partitioning of the ribosomal DNA small subunit and its effects on the phylogeny of the Anopheles punctulatus group. Insect Molecular Biology 9: 515-520.

Beebe NW, Cooper RD, Morrison DA, Ellis JT (2000) A phylogenetic study of the Anopheles punctulatus group of malaria vectors comparing rDNA sequence alignments derived from the mitochondrial and nuclear small ribosomal subunits. Molecular Phylogenetics and Evolution 17: 430-436.