notes on evolutionary biology papers/programs and other stuff: a non-frequent approach

Monday, June 18, 2007

rename it with a script

Although there are nice little programs for OSX that rename file names and extensions, like Renamer4Mac, NameChanger and FileSorter, it's always good to have something simple handy, like a script.

in AppleScript: Nem

in Perl: here and here (Linux)

my favorite is a loop in Unix to rename file extensions:

1) if you know what your extensions are:


#!/bin/bash

for i in *fasta
do
mv "$i" "`echo $i | sed -e 's/fasta/fas/'`"
done

for i in *fas
do
cat "$i" | sed -e 's/\.fasta\"/\.fas\"/g' > out
mv out "$i"
done


2) if you prefer an interactive script that will ask you what extension names you want to change from/to:


#!/bin/bash

echo -n "enter old: "
read old
echo -n "enter new: "
read new

for i in *.$old
do
mv "$i" "`echo $i | sed -e "s/$old/$new/"`"
done


The shell scripts were kindly written by my friend Ricardo Baratto

Saturday, June 16, 2007

Automation and evaluation of NCPA

Following up on the previous posting on two programs that automate the inference process of Nested Clade Phylogeographic Analysis (NCPA), Panchal & Beaumont create a framework of automated NCPA. Their simulations show that NCPA has a high tendency for false positives. More research is needed, of course, on real-life data.

Panchal M, Beaumont MA. (2007) The automation and evaluation of Nested Clade Phylogeographic Analysis. Evolution 61(6):1466-1480.

Tuesday, February 6, 2007

Automating Nested Clade Analysis

TCS and GeoDis are the programs to use for NCA, but recently two programs came out that automate NC inference: AUTOINFER and ANeCA.

Addendum (30 Oct 2007)
Panchal & Beaumont (2007) of ANeCA report that Ai-bing Zhang of AUTOINFER has noted that there are some issues in the program that require resolution and that it has temporarily been withdrawn.

Friday, February 2, 2007

Trees: stop fighting!

Tree reconciliation in host-parasite coevolution or in gene-tree fitting has been a long-standing issue in evolutionary biology. Here's some programs that try to bring peace...

TreeMap: for cophylogeny mapping.

TreeFitter: for MP tree-fitting.

SoftParsMap: maps gene trees onto species trees using soft parsimony.

gtp: species tree reconciliation and gene tree parsimony.

UREC: for computing unrooted gene and rooted species tree reconciliation.

CopyCat: easy & fast access to co-phylogenetic analyses. has a wrapper for ParaFit that tests for the association of host and parasite phylogenies.

PriMETV: visualizes tree-within-tree phenomena.

bioinformatics dashboard widgets

Check out ~20 bioinformatics dashboard widgets for OSX Tiger. everything from genetic codes, aminoacid/nucleotide properties, to NCBI BLAST and Entrez. cool!

See the Tree?

Some programs I use to display trees in OSX. Some allow the user to modify trees.

TreeViewX: the industry standard for simple tree visualization.

TreeEdit: views and manipulates trees, re-roots, simulates trees.

FigTree: nice graphical tree viewer.

TreeIllustrator: not only it displays and fiddles with trees, but also has a built-in ToL browser/search engine.

TreeStat: calculates tree statistics (balance, shape, length, popgen).

Phylodendron: draws trees on a webserver or locally (Java app).

TreeJuxtaposer: displays and compares/compresses trees. needs GL4java.

ArboDraw: tree editing with sequence annotation functionality.

TreeMaker: builds taxonomies with species richness data.

TreeSetViz: visualizes tree sets in treespace as a Mesquite module.

Wednesday, December 6, 2006

2 new journals for 2007

Two new journals are to be launched in 2007:

Evolutionary Biology, following the book serial originally founded by Theodosius Dobzhansky.

HFSP Journal - Frontiers of Interdisciplinary Research in the Life Sciences, published by the Human Frontier Science Program. Six months following publication, papers will be open-access, leaving the publication copyright to the authors.

Tuesday, November 28, 2006

"Beer goggles" effect explained

Beauty is in the eye of the beer-holder. A formula built by researchers at the University of Manchester, UK, spits out a score ranking the drinkers' (mis)perception of beauty. The calculation factors in not only the the amount of booze consumed, but also the light conditions, the amount of smoke in the room, visual acuity, and distance from the person of interest.

BBC News online article

Selection in murid noncoding DNA

In the November issue of PLoS Genetics Gaffney & Keightley present results from their in silico examination of the rat and mouse genomes. They find selection to be acting three times more (in absolute number of sites) in noncoding than in coding sites. Most of these constrained noncoding sites are found more than 5kb away from known protein-coding genes. Intron sites believed to be functionally important are observed to be more concentrated near the 5'-end of genes, providing more evidence for a role of such intron parts in gene regulation. Intergenic regions appear to be harboring twice the number of deleterious mutations found in genes.

Gaffney DJ, Keightley PD. (2006) Genomic selective constraints in murid noncoding DNA. PLoS Genetics 2(11):e204.

Supergene controls color in buterflies

In the October issue of PLoS Biology Joron et al. report that a "supergene" locus controls color patterning in three Heliconius butterfly species.

Joron et al. (2006) A conserved supergene locus controls colour pattern diversity in Heliconius butterflies. PLoS Biology 4(10):e303.