Sequence Alignments

 

This page gives access to the data files used in various of the publications listed under
Molecular Phylogenetics Publications in the bibliography of AssProf David Morrison.

Most of the data files have aligned sequences in NBRF format (including IUPAC ambiguity codes).
This is a portable format, which can be easily converted to other formats.

 
Holmdahl, O.J.M., Morrison, D.A., Ellis, J.T., and Huong, L.T.T. (1999) Evolution of ruminant Sarcocystis (Sporozoa) parasites based on small subunit rDNA sequences. Molecular Phylogenetics and Evolution 11: 27-37.
Ellis, J.T., Holmdahl, O.J.M., Ryce, C., Njenga, J.M., Harper, P.A.W., and Morrison, D.A. (2000) Investigations on the molecular phylogeny of Besnoitia species and the genetic relationships between Besnoitia of cattle, wildebeest and goats. Protist 151: 329-336.
Beebe, N.W., Cooper, R.D., Morrison, D.A., and Ellis, J.T. (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.
Mugridge, N.B., Morrison, D.A., Jäkel, T., Heckeroth, A.R., Tenter, A.M., and Johnson, A.M. (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.
Höglund, J., Morrison, D.A., Divina, B.P., Wilhemsson, E. and Mattsson, J.G. (2003) Phylogeny of Dictyocaulus (lungworms) from eight species of ruminants based on analyses of ribosomal RNA data. Parasitology 127: 179-187.
Morrison, D.A., Bornstein, S., Thebo, P., Wernery, U., Kinne, J. and Mattsson, J.G. (2004) The current status of the small subunit rRNA phylogeny of the coccidia (Sporozoa). International Journal for Parasitology 34: 501-514.
Morrison, D.A (2006) Phylogenetic analyses of parasites in the new millennium. Advances in Parasitology 63: 1-124.

Note: These data sets are in Nexus format, and include the commands used for the data analyses.

Morrison, D.A. (2007) Increasing the efficiency of searches for the maximum-likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences. Systematic Biology 56: 988-1010.

Note: These data sets are in Nexus format, from the journal's web page.

Morrison, D.A. (2009) A framework for phylogenetic sequence alignment. Plant Systematics and Evolution 282: 127-149.
Morrison, D.A. (2009) Evolution of the Apicomplexa: where are we now? Trends in Parasitology 25: 375-382.

Note: The data set is in Nexus format, with a MrBayes block identifying the regions of ambiguous alignment, the regions of expansion and contraction, the paired sites, and the sites not used in the data analyses.

Whipps, C.M., Fournie, J.W., Morrison, D.A., Azevedo, C., Matos, E., Thebo, P. and Kent, M.L. (2012) Phylogeny of fish-infecting Calyptospora species (Apicomplexa: Eimeriorina). Parasitology Research 111: 1331-1342.

Note: The data set is in Nexus format, with a MrBayes block identifying the regions of ambiguous alignment, the regions of expansion and contraction, the paired sites, and the sites not used in the data analyses.

Schnittger, L., Rodriguez, A.E., Florin-Christensen, M. and Morrison, D.A. (2012) Babesia: a world emerging. Infection, Genetics and Evolution 12: 1788-1809.

Note: The data sets are in Nexus format, with a MrBayes block. For the rRNA data this identifies the regions of ambiguous alignment, the regions of expansion and contraction, the paired sites, and the sites not used in the data analysis.

Tydén, E., Engström, Morrison, D.A., Höglund, J. (2013) Sequencing of the β-tubulin genes in ascarid nematodes Parascaris equorum and Ascaridia galli. Molecular and Biochemical Parasitology 191: 38-43.

 
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