An evolutionary event where two identical changes occur independently. For instance when two homologous sequences possess an isoleucine at a particular position, and both isoleucines are substituted for leucines. The ancestral state is the same in both instances and the new character state is the same. The difference between this type of event and a convergence lies in the identity of the ancestral state.
This is a gene from the same homologous super family found in another part of the genome of a particulat taxon. Paralogs are the result of a gene duplication, not a lineage splitting event.
This program is the most important program for those who wish to reconstruct phylogenetic relationships. It is a stand-alone program and runs on Apple macintosh™, Windows™ and UNIX operating systems. It can deal with DNA and protein sequences as well as morphological data or any binary or multi-state character data. It is maintained by David Swofford and is available for purchase from Sinauer Associates.
A branching diagram that links entities by estimates of overall similarity. Usually constructed using UPGMA cluster analysis.
The name of a package of programs for inferring phylogenies. More information
may be found at the PHYLIP webpage:
http://evolution.genetics.washington.edu/.
This is the scientific discipline of resolving the relationship among and between organisms. It is one of the three branches of Systematics.
A tree that depicts inferred historical relationships among entities. Differs from a cladogram in that the branches are drawn proportional to the amount of inferred character change.
Homology of repeated sequences that are subject to concerted evolution.
An ancestral character state.
Permutation Tail Probability test. This is a matrix randomisation test. The columns of a matrix are randomised so that the consensus sequence and the composition for any particular column is maintained, but any signal is lost. Any measure of a tree (say tree length) should be much worse from the permuted data than from the original data except when the original data is no better than random in the first place.
An Adenine or a Guanine nucleotide.
A Cytosine or a Thymidine nucleotide.
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