Resources

Molecular Biology

Links to protocols, programs & guides for molecular biology, e.g., sequence analysis, tree building, TRFLP analysis, available on the web.

Sequence Analysis & Tree Building

Geneious
This is a program for all OS (Windows, Linux and Mac) for sequence analysis, etc. I have been using the Pro version for a few weeks and so far I am really happy with it. I like the sequence viewing, the contig assembly and the Blast features. The program allows you to batch BLAST your sequences against the NCBI database from within the program. You can tell it how many results you want to get back and they are delivered back to the program. VERY, VERY useful!!

Mothur
An open-source, software that fills the bioinformatics needs of the microbial ecology community. This is above and beyond the best software to use for dealing with 16S rRNA data sets. It can be used for clone libraries or pyrosequencing data. It includes programs for aligning sequences, grouping into OTUs, performing rarefaction, and other statistical analyses. It can be used on Mac, PC, and Linux and the only limiting step is being comfortable with running a command line-based program. It is worth the learning curve to get this running.

FastGroupII
FastGroupII is a web-based tool for analyzing sequence data. It is specifically designed for dealing with large SSU rRNA sequence clone libraries. It contains several different algorithms for trimming sequences and grouping phylotypes based on sequence similarity. I used this program quite a bit in my work up until 2011, now I have switched to using Mothur because I found that the clustering was not perfect and further analysis showed that what were named as different OTUs were in fact the same. I think that this can be useful but keep in mind that the output should be checked with other methods.

greengenes
Site specific for aligning and working with ribosomal sequences. The align function is excellent for aligning sequences to nearest neighbors and incorporates rRNA secondary structure in the algorithm.

UniFrac
This is an excellent program for analyzing microbial community sequence data. It is free online and very easy to use and also available in Mothur.

Fast UniFrac
Fast UniFrac is a new version of UniFrac that is specifically designed to handle very large datasets. Like UniFrac, Fast UniFrac provides a suite of tools for the comparison of microbial communities using phylogenetic information.

BioEdit
This is a really nice (free) program for sequence manipulation. Unfortunately it is only available for PC.

TreeView
I find that TreeView is a very nice program for viewing trees and exporting them as images. It is available for both Mac and PC but there are few options for text formatting and no options for illustrations.

TreeDyn
I just heard about this program and have not tried it out. It looks promising.

PAUP* 4.0 I am not an expert at PAUP and have had difficulty in remembering commands, etc. for building phylogenetic trees. Here are a few links that I found useful when battling through PAUP:

4Peaks
4Peaks is a program for visualize and edit their DNA sequence files on Mac OS X. I downloaded this program but have not been using it very much. It seems to be useful but not for large data sets. Brought to you by the same programmers of Papers.

eBio Tools
Another program for sequence analysis in Mac OS X. I use this to view fasta files quickly on my Mac but I haven't used it for any other purpose.

Terminal Restriction Fragment Length Polymorphism (TRFLP) Analysis

PAT-TRFLP: Phylogenetic Assignment Tool for TRFLP PAT-TRFLP is a web-based tool for analyzing of TRFLP profiles of microbial communities. This is a very nice application that is easy to use! I like the fact that it is available on the web and able to be used by all OS users. Another bonus for this program: the user can define the database for matching profiles.

FragSort
The TRFLP Fragment Sorter Suite is a Windows based program for identifying peaks from TRFLP profiles. This program is excellent although there are a few stumbling points for getting it running for a user-specified database. Once up and running it is easily used. Two great features: numerous algorithms for incorporating fragment sizing error and uses a user-defined database for matching peaks.

Denaturing Gradient Gel Electrophoresis (DGGE) Links

DGGE Help
This is a blog maintained by Dr. Stefan Green. The DGGE Help website contains guides and discussions for using and troubleshooting DGGE techniques.
Stefan Green's website: www.stefangreen.com

Literature Resources

Useful resources for finding papers and referencing literature

Resources for literature searches:

Online literature searches:

Helpful tools for citing and organizing references:

EndNote
Software for organizing and preparing bibliographies. I really like using EndNote but it takes a bit of practice and patience to get used to it. I can't imagine writing papers without it.

Papers2
This is a Mac based program for organizing and viewing PDFs of papers. I have been using this program for almost a year and have been extremely happy with it. I really like the viewing modes and the ability to search and organize my references. Another excellent feature is the option to export citations from PDFs in Papers for use in EndNote. The programmers are also very helpful and provide a nice discount for students. Another great feature is being able to search for articles from Papers and directly import the new references into your library. Also available for iPhone and iPad