...some more detail about the CIPRES services, which would include alignment, phylogeny inference, and supertrees.
4 KB (664 words) - 11:09, 5 September 2007
...ion, I should find a recently published paper that includes an analysis of phylogeny and dN/dS for some sequence family (doesn't matter which), and that has sup
11 KB (1,762 words) - 11:45, 5 September 2007
...OTUs, long names that would be corrupted during subsequence alignment and phylogeny reconstruction, machine-dangerous characters such as space and punctuations
...ar phylogenies. Nature 425, 798-804 (23 October 2003). (Note: yeast genome phylogeny using 106 orthologs)
34 KB (4,831 words) - 16:08, 8 November 2011
...http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1679813 A Fungal Phylogeny based on 42 Genomes]). This user story starts with a large number of genome
9 KB (1,461 words) - 16:23, 3 March 2008
...>Treebase export. rbcL sequence data with tree from analysis of liverwort phylogeny by Lewis, et al., 1997. No TAXA block. No branch lengths. </td>
Maddison, W.P. and D.R. Maddison. 1992. MacClade, Version 3: Analysis of Phylogeny and Character Evolution. Sinauer Associates, Sunderland, Mass.
41 KB (6,423 words) - 02:20, 30 March 2008
...are planning to develop APIs for BioJava. Especially, we will focus on the phylogeny reconstructing methods such as UPGMA, Maximum Parsimony, and Maximum Likeli
33 KB (4,999 words) - 21:12, 22 October 2010
...nces of LTR retrotransposons as the OTUs. Development will assume a single phylogeny per database. The variables for database name, user name, user password, an
Modify an existing phylogeny in the database. This will use -x, -c, and -v as command line arguments to
20 KB (2,741 words) - 16:23, 23 October 2007
...ficiently and intuitively by weaved together giving greater insight to the phylogeny of different organisms.
# Create a track to view a phylogeny tree in line with the genome browser. It would be ideal to paint the tree
8 KB (1,310 words) - 16:31, 21 December 2007
* Determine correlation of a phylogeny with other variables
* Tree of life: whole-genome phylogeny and horizontal transfer
16 KB (2,329 words) - 11:27, 5 September 2007
* Phylogeny format and structure
22 KB (2,696 words) - 09:19, 10 December 2007
* representation of quantitative traits along with phylogeny (dotchart.phylog, symbols.phylog, table.phylog)
* Heavy: instead of simply containing data of a phylogeny, the class 'phylog' stores various other information (Abouheif's 'A' matrix
23 KB (3,588 words) - 22:22, 28 December 2007
** graphical representations: phylogeny represented alone (plot.phylog, radial.phylog) or together with quantitativ
10 KB (1,339 words) - 13:17, 16 July 2008
'''How do I input data corresponding to the tips of my phylogeny into R?'''
...umn should represent the names of your taxa exactly as they appear in your phylogeny (see previous section). The second and any subsequent columns of the datafi
2 KB (303 words) - 15:04, 6 February 2008
'''How do I input a phylogeny into R?'''
...o" (more specifically, objects of class "phylo"). Luckily, converting your phylogeny to "phylo" representation is easy.
3 KB (562 words) - 15:03, 6 February 2008
...ecute some of the worked examples below yourself, save the sample Geospiza phylogeny and dataset ([[Media:geospiza.rda|geospiza.rda]]) to your working directory
== How do I designate a specific taxon to be the root of my phylogeny? ==
10 KB (1,661 words) - 11:48, 15 December 2008
The evolution of a discrete character along a branch of a phylogeny can be modeled as a Markovian process, where the probability of moving the
4 KB (706 words) - 15:10, 6 February 2008
...g as your row names in your dataframe (mydata) match the tip labels in the phylogeny (mytree$tip.label) you can associate the data with the correct tip by:
5 KB (685 words) - 15:16, 6 February 2008
...have installed and loaded ape into your R session and loaded the Geospiza phylogeny and tip data into memory.
IMPORTANT. The row.names of your dataframe must match the tip.labels of your phylogeny. In the example above, the row.names for geodata will match the tip.labels
15 KB (2,313 words) - 12:22, 12 February 2008
...ape. This will calculate branching times associated with each node in the phylogeny and place them in an object.
...eeds the string of branching times to be ordered from 1st (earliest in the phylogeny) to last (most recent), if your string is not ordered it will automatically
6 KB (881 words) - 15:18, 6 February 2008
...s an application for the [[#Phylogeny plotting for the R package phylobase|Phylogeny plotting for the R package phylobase idea]].
===Phylogeny plotting for the R package phylobase===
56 KB (8,424 words) - 21:11, 22 October 2010