Trees of whole genomes, but locally

With increasing use of Next-generation sequencing methods, whole genomes of multiple species as well as closely related strains or populations are being generated. Sophisticated models to interpret this data that use our current knowledge of population dynamics and molecular processes are being used extensively.

The general idea is to be able to distinguish the population histories of various parts of the genome. The phylogenies of different parts of the genome might differ based on various functional constraints. Hence, building a single consensus tree for the entire genome will average over these local effects. To be able to overcome this limitation, many methods are being proposed to identify local phylogenies across the genome.

The program Saguaro, from Science for Life Laboratory and Broad Institute, is capable of using SNP data in VCF format or whole genome assembly alignments in MAF format to partition the genome based on local phylogenetic information. The method and its use on few example datasets is described in Unsupervised genome-wide recognition of local relationship patterns. 

Temporary variables – 5 common mistakes

Temporary variables are a type of variable which are used to store a value obtained from a particular computation or data source, which will be used in a later stage of the program. Although temporary variables serve very useful purposes, they can be the cause of major software bugs that seem to occur inexplicably. The common coding or programing mistakes associated with temp variables:

1. Loss of precision: The use of a lesser precision variable for a temp variable can lead to loss of precision which leads to bugs.


Ex: Using a Integer variable to store the result of a calculation that includes a higher precision like float or double. Even in langauages like java by explicitly typecasting(coders mistake).


2. Value out of bound: Similar to the first mistake but occurs in arrays and strings. Can mainly lead to rendering mistakes.


Ex:While using the last few characters of a string or last few values of an array.


3. Multiple inputs: The temporary variable value can get overwritten by incorrect code even before its value is used.

Ex: Status being changed even before the code required to be executed in previous status completes execution.

4. Excessive memory usage:The excessive use of temporary variables can have an impact on the memory usage of the program.

Ex:Using temp variables even when they are not absolutely needed.

5. No exception handling ( Like Null value, negative value) :The temporary variables can behave in weird ways if various exceptional cases are not anticipated and guarded against.

Ex:Not guarding against storing negative values in temp variables later used as array index etc.

Software program to make a Quiz - multiple choice

If you want to create a quiz with multiple choice questions, the Quiz program by Luzius Schneider seems to do the job. The program is free to use as long as we are OK to share the questionnaires we create using the software. The program makes use of the Borland Database engine to easily store and retrieve the questions. There are options to set time limits, provide hints about the answer and even further explanations for an answer if you are interested.

Quiz also has few shareware upgradations which run on the network, a intranet or even the internet.