ash211 gtfold issues - Githubissues

ash211 / gtfold

GTfold is a fast, scalable multicore code for predicting RNA secondary structure and is one to two orders of magnitude faster than the de facto standard programs and achieves comparable accuracy of prediction.

http://gtfold.sourceforge.net/

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issues

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fixed issue 17, please merge

#35 pgaurav opened 13 years ago
0
Put something in the README file or remove

#34 shelswenson opened 13 years ago
0
Release documentation (how to do a release)

#33 shelswenson opened 13 years ago
0
Create release script and package

#32 shelswenson opened 13 years ago
0
.spec file

#31 shelswenson opened 13 years ago
0
License fixes

#30 shelswenson opened 13 years ago
0
autoconf/make fixes

#29 shelswenson opened 13 years ago
0
Output terms explaining difference between sum of loop energies and total energies

#28 ash211 closed 13 years ago
1
rewrite branch is not handling a fasta file properly

#27 shelswenson closed 13 years ago
2
Is it ok to link to http://www.bioinformatics.org/sms/iupac.html ?

#26 ash211 closed 13 years ago
2
--bpp flag is ridiculously extremely slow

#25 ash211 opened 13 years ago
0
Create test harness

#24 ash211 opened 13 years ago
0
Build other arrays from bottom up

#23 ash211 closed 13 years ago
1
Can't run without compiling out openmp

#22 ash211 closed 13 years ago
3
Rewrite branch isn't parallelizable

#21 ash211 closed 13 years ago
3
Missing constraints in rewrite branch

#20 ash211 closed 13 years ago
2
Load back the UI from release to rewrite

#19 ash211 closed 13 years ago
2
rewrite branch can't read FASTA sequences

#18 ash211 closed 13 years ago
2
Clearly report External Loop energy

#17 shelswenson closed 13 years ago
1
generate ct file in the current directory

#16 pgaurav opened 13 years ago
2
Create --verbose option

#15 shelswenson closed 13 years ago
2
add -o option

#14 shelswenson closed 13 years ago
1
printing sequence to console

#13 shelswenson closed 13 years ago
1
ct file names

#12 shelswenson closed 13 years ago
1
j-i >= 4

#11 spoznan closed 13 years ago
1
pseudoknots in constraints

#10 spoznan opened 13 years ago
0
no more --quiet (and exit if ambiguous)

#9 shelswenson closed 13 years ago
2
k=0 in constraints file should be invalid

#8 spoznan closed 13 years ago
1
--limitCD not working

#7 shelswenson closed 13 years ago
2
Turner04 option

#6 spoznan closed 13 years ago
1
subopt output

#5 shelswenson closed 13 years ago
2
default subopt

#4 shelswenson closed 13 years ago
2
install-sh still not executible

#3 shelswenson closed 13 years ago
1
Single-letter options

#2 shelswenson closed 13 years ago
1
README

#1 shelswenson closed 13 years ago
1