Hillis DM. 1996. Inferring complex phylogenies. Nature 383: 130-131. Triangles: parsimony Squares: neighbor-joining (under specified model) Circles: UPGMA
Designing your phylogenetic analysis Choice of data (morphology/behavior/molecules ) Choosing your ingroup/outgroup taxa Choosing the amount of information More genes or more taxa?
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Gene accumulation Curves (Rarefied with 50 random addition replicates)
ESTs processing Raw trace files need to be processed: trace2dbest EST reads are then assembled using PartiGene (with original quality files allowed) PartiGene calls CLOBB to assign sequences to clusters of like sequences and PHRAP to assemble the EST sequences assigned to each cluster into a contiguous sequence for that cluster The single contiguous sequence for each cluster is then translated with prot4est
Orthology assignment A local database of all Homo sapiens, Canis familiaris, Gallus gallus, Drosophila melanogaster, and Anopheles gambiae sequences that have orthology assignments in Homologene is constructed Masked sequences were queried against these sequences with blastp The blast results were passed to TribeMCL for Markov Chain Clustering (MCL). (The MCL inflation parameter was varied in intervals of 0.1 from 1.4 to 2.5 to identify the value that generated the maximum number of clusters) TribeMCL groups that had no sequences from the homologene dataset were discarded, as were groups that had homologene sequences that were assigned to multiple TribeMCL groups Only groups with sequences from at least 33% of the taxa are preserved The number of sequences for each species represented within each group is calculated, and groups with a median greater than one are discarded
EST data set After passing the taxon sampling and orthology criteria, we obtained 196 genes for 56 species On average, each species was represented by 48% of the genes The combined matrix consists of 32,975 amino acids (19,362 positions are parsimony-informative) Our matrix of 196 genes contains only 50 of the genes included in the 146-gene matrix of Philippe et al. (2005)