User: kaustubh.patil

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Posts by kaustubh.patil

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Bioruby Read Fasta Multithreaded
... Hi, While writing a multithreaded application using bioruby I ran into a problem namely, I was not able to read and parse FASTA files. The error message I get is "uninitialized constant Bio::FastaFormat". The error reproduction code is shown below (both fasta files are approx 60 MB with ~150000 seq ...
fasta read written 8.1 years ago by kaustubh.patil0 • updated 8.1 years ago by Istvan Albert ♦♦ 84k
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Cophenetic Correlation And Tree Comparison
... Hi all, I have trouble understanding some recent observations. The scenario is like this; I have a cophenetic matrix C (inferred using a given non-binary tree). Then I have n distance matrices D{1..n} (defined over same set of leaf nodes as the given tree). I want to choose a distance matrix that i ...
phylogenetics correlation tree comparison written 8.2 years ago by kaustubh.patil0
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Blastclust Gives Segmentation Fault
... Hi, I want to use blastclust program from standard standalone blast installation. I tried to cluster 26 strains of E. Coli; blastclust -i e_coli.fna -o outfile -p F -L .9 -b T -S 95 It gave the following output; Jan 17, 2011 12:43 PM Start clustering of 26 queries Segmentation fault Then I tr ...
sequence clustering written 9.4 years ago by kaustubh.patil0 • updated 8.2 years ago by Hamish3.1k

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