search for: phylip

...d with --delete . I have the following directory structure on server A: ls -lR software software: total 238 drwxr-xr-x 2 biolord bioinf 1024 Sep 20 10:49 EMBOSS/ lrwxrwxrwx 1 biolord bioinf 6 Feb 5 2003 MSE -> EMBOSS/ lrwxrwxrwx 1 biolord bioinf 6 Feb 5 2003 PHYLIP -> EMBOSS/ ... lrwxrwxrwx 1 biolord bioinf 6 Feb 5 2003 TOPO -> EMBOSS/ ... software/EMBOSS: total 87942 -rw-r--r-- 1 biolord bioinf 551090 Jul 15 18:54 DOMAINATRIX-1.0.0.tar.gz -rw-r--r-- 1 biolord bioinf 12100223 Jan 21 2003 EMBOSS-2.6.0.tar.gz -rw-r--r-- 1 biol...

...e matrices with R. I would like to create a XY plot of these matrices and do some linear regression on it. But, I am a bit new to R, so i have a few questions (I searched in the documentation with no success). The first problem is loading a distance matrix into R. This matrix is the output of a the Phylip program Protdist and lookes like this: 5 n_crassa 0.000000 0.690737 0.895257 0.882576 2.365386 c_neufor 0.690737 0.000000 0.956910 0.979988 2.103041 a_thaliana 0.895257 0.956910 0.000000 1.003668 2.724847 pompep 0.882576 0.979988 1.003668 0.000000 2.065202 s_cerevis...

Hello, My name is Sivan and I am a master degree student in statistics,my problem is as follows: I have a dataset containing gene sequences and I would like to create a phylogenetic tree from it. The problem that I can't seem to find a function to do this kind of operation. I read the ape package manual and I haven't found a command that takes raw data and turns it into a tree. does anyone

...d on sequence similarities. There is a wide range of sequences in the set, some of which are homologous to other sequences in the set. I want to use clustering to identify these groups. If the sequences were related and good be trimmed to the same length, I would do an alignment and then use phylip (or some other distance method) to create a distance matrix, but since my sequences are unrelated and cannot be trimmed to the same length, I am at a loss for what to do. For a set with so many unrelated sequences of different lengths, the only thing I have been able to is an all-against-all B...

dear group members, I am looking for a function that assess the stability of cluster. The result of hclust function is an hclust object which can be plot as a dendrogram. However to have confidence in the tree topology usualy bootstap is applied. I understand that I can apply bootstarp on the original data and then run hclust(dist() ) as much as I resampled but how to comapre the topologies the I

Hi I am looking for a package that 1. reads in a phylogenetic tree in NEXUS format 2. given two members/nodes on the tree, can return the distance between the two using the tree. I came across the following packages on CRAN ouch, ape, apTreeShape, phylgr all of which seem to provide extensive range of functions for reading in a Nexus-format tree and performing phylogenetic analyses, tree

...erface, and initial support for the RKward GUI; - even stronger bioinformatics/biology support than before: BioConductor, arb, biofox, bioperl, biopython, blast2, boxshade, bugsx, clustalw, fastdnaml, fastlink, garlic, gromacs, hmmer, loki, mipe, molphy, muscle, ncbi, phylip, rasmol, readseq, seaview, t-coffee, textopo, and more; - continued strong mathematics / computational algrebra support: axiom, blacs, calc, euler, gap, giac, mathomatic, maxima, pari, scalapack, scilab, texmacs, yacas, yorick; - strong visualization / graphics...

...erface, and initial support for the RKward GUI; - even stronger bioinformatics/biology support than before: BioConductor, arb, biofox, bioperl, biopython, blast2, boxshade, bugsx, clustalw, fastdnaml, fastlink, garlic, gromacs, hmmer, loki, mipe, molphy, muscle, ncbi, phylip, rasmol, readseq, seaview, t-coffee, textopo, and more; - continued strong mathematics / computational algrebra support: axiom, blacs, calc, euler, gap, giac, mathomatic, maxima, pari, scalapack, scilab, texmacs, yacas, yorick; - strong visualization / graphics...

...ve, an early release of the RKward GUI and more. - continued strong bioinformatics/biology support: BioConductor, arb, biofox, bioperl, biopython, blast2, boxshade, bugsx, clustalw, fastdnaml, fastlink, garlic, gromacs, hmmer, loki, mipe, molphy, muscle, ncbi, phylip, rasmol, readseq, seaview, t-coffee, textopo, ImageJ, and more; - continued strong mathematics / computational algrebra support: axiom, blacs, calc, euler, gap, giac, mathomatic, maxima, pari, scalapack, scilab, texmacs, yacas, yorick; - continued strong visual...

...ve, an early release of the RKward GUI and more. - continued strong bioinformatics/biology support: BioConductor, arb, biofox, bioperl, biopython, blast2, boxshade, bugsx, clustalw, fastdnaml, fastlink, garlic, gromacs, hmmer, loki, mipe, molphy, muscle, ncbi, phylip, rasmol, readseq, seaview, t-coffee, textopo, ImageJ, and more; - continued strong mathematics / computational algrebra support: axiom, blacs, calc, euler, gap, giac, mathomatic, maxima, pari, scalapack, scilab, texmacs, yacas, yorick; - continued strong visual...

...gths. The nodes matrix provides an easy access for developers to further manipulate the tree, while the tree string provides interface with other phylogenetic R packages such as "ape". The input/output functions can also be used to change the format of tree files between NEXUS and PHYLIP. Some basic functions have already been established in the package for manipulating trees such as deleting and swapping nodes, rooting and unrooting trees, changing the root of the tree. The package also includes functions such as "consensus", "coaltime, "popsize",...