I am looking for some software to analyse clones for some work I am doing with quasispecies.
It has been suggested to me that I can calculate my Hamming distances (+ confidence intervals) manually but with roughly 1,000 clones to analyse, this is not appealing.
If it is the case that I have to do it manually, is from a consensus sequence that I have to calculate them?
I have been using Mega4.0 for my phylogenetic trees but this calculates only p-values for genetic distances. I have also downloaded some of Stuart Ray's freeware but must admitt that I haven't been able to give me the figures I need.
Can anyone recommend a user friendly platform for calculating Hamming distances/ Shannon entropy etc for multiple sequence alignments?
All advice much appreciated.
Dan
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2 replies to this topic
#2
feilr
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Posted 16 December 2010 - 12:28 AM
NoeClone: The first next-generation molecular cloning tool on the market
NoeClone, our flagship product, integrates cloning design, map and flowchart drawing, sequence analysis, and result presentation in one coherent system as the "Office for the biologist".
Benefits of using cloning software
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▼ The NoeClone advantages
● Direct and easy manipulation of individual map in the same window
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● Strategic design flowchart with gel simulation
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● Multiple sequence alignment and many other analysis tools
● Integrated database with keyword and local blast search functions
you can download at http://www.noegen.co...downloading.php
NoeClone, our flagship product, integrates cloning design, map and flowchart drawing, sequence analysis, and result presentation in one coherent system as the "Office for the biologist".
Benefits of using cloning software
● Improve work efficiency, save time
● Create precise experimental design with graphical displays, avoiding costly mistakes
● Manage cloning records as critical company assets for intellectual property and knowledge base
● Facilitate data exchange, collaboration, teachingand training within and cross organizations
▼ The NoeClone advantages
● Direct and easy manipulation of individual map in the same window
● Completely interactive graphic maps and sequences
● Multiple plasmid maps in a single view
● Multiple fragment cloning
● Strategic design flowchart with gel simulation
● High-throughput cloning
● Multiple sequence alignment and many other analysis tools
● Integrated database with keyword and local blast search functions
you can download at http://www.noegen.co...downloading.php
#3
Adrian K
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Posted 16 December 2010 - 04:49 PM
well, this is not free...
Expecting the world to treat you fairly because you are a good person is like expecting the lion not to attack you because you are a vegetarian.
..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...
"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong
"It's all just DNA. Do it."---phage434
..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...
"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong
"It's all just DNA. Do it."---phage434
