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Removal of Bio::Tools::Phylo::PAML.pm and related modules, tests, and docs
2017-09-08
C
a
rnë Draug
Removal of B
i
o::Tools::Phylo:
:
PAML
.
p
m
and related mod
u
l
es
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Ca
r
në Draug
Bio::PhyloNetwork::muV
e
ct
o
r: revert no
n
-typo fro
m
54c99cf411
commit
|
commitdiff
|
tree
2017-08-30
Carnë Draug
mai
n
t: fix m
u
lt
i
p
l
e
typos identified by
l
int
i
an
commit
|
commitdiff
|
tree
2015-11-29
Carnë Draug
bp_pairwis
e
_kaks
.
pl:
d
o
not mix sp
a
c
e
and tabs
for
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
C
arnë Draug
Bio:
:
Align::Utilities - remove u
s
age
o
f /r opt
i
on
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Fix nonsense
in code comments
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë D
r
aug
Bio::Align::Utili
t
ies - follow some pe
r
l
best pract
i
c
e
s
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Bio:
:
A
l
ign::U
t
ilities
-
new function
mo
s
t
_
common_seq
u
enc
e
s
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Bio::SimpleAlign - fo
l
low some perl best
practices
commit
|
commitdiff
|
tree
2013-04-04
Carn
ë
Draug
mai
n
t
: r
e
move files that have been moved to
a
se
p
arate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë
D
r
a
ug
maint: update Changes aft
e
r
r
e
moving fi
l
e
s fr
o
m Bio
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Dra
u
g
ma
i
nt: remov
e
files that ha
v
e bee
n
moved to a
separate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Draug
tests: mov
e
te
s
ts from Root
t
o Assembly
a
nd
S
e
q
IO
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë Draug
maint: rem
o
ve hard tabs and trail
i
ng whitespac
e
commit
|
commitdiff
|
tree
2013-03-28
Carnë
Draug
t
es
t
s
for inheritan
c
e should belon
g
on th
e
chil
d
clas
s
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë Draug
r
emove h
a
rd
t
a
b
s and
t
rai
l
i
n
g whitespace
from some
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë Draug
Annotation: fix
t
yp
o
on test
commit
|
commitdiff
|
tree
2013-03-26
Carnë Dra
u
g
Bio::
C
luster::Seq
u
enceFamily - bug fixes and performance
commit
|
commitdiff
|
tree
2013-03-26
Carnë D
r
a
u
g
doc: fix indent
a
tion, rem
o
v
e har
d
tab
s
a
n
d trai
l
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2013-03-21
Carnë Drau
g
recover GenericWebAg
e
nt from Bio-EUti
l
i
t
i
es
commit
|
commitdiff
|
tree
2013-03-13
Carnë
D
raug
split Bio-Biblio into
a separate distribu
t
ion
commit
|
commitdiff
|
tree
2013-03-12
Carnë D
r
aug
M
e
r
ge pull request #53
f
rom bv
a
isvil/master
commit
|
commitdiff
|
tree
2013-03-06
Carn
ë
Drau
g
Bio::
P
er
l
- fix inde
n
tati
o
n (remove t
a
bs, and weird
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Ca
r
në Dr
a
ug
Don
'
t use a separate default scalar
w
hen there's a
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Carnë
D
raug
follow perl recomm
e
ndatio
n
s:
commit
|
commitdiff
|
tree
2013-03-04
Carnë
D
r
aug
fix indentati
o
n (rem
o
ve tabs, and wei
r
d
3
sp
a
ces inden
t
ation)
commit
|
commitdiff
|
tree
2013-03-04
Carnë Dr
a
u
g
fol
l
o
w perl
r
e
commendations:
commit
|
commitdiff
|
tree
2013-03-04
Car
n
ë Drau
g
use until instead of wh
i
le(1
)
{l
a
st
i
f
.
.
.
}
commit
|
commitdiff
|
tree
2013-03-04
Carnë Dr
a
ug
fi
x
in
d
entation (remove ta
b
s
, 3 spa
c
e
a
nd 2 spac
e
indentation)
commit
|
commitdiff
|
tree
2013-02-11
Car
n
ë Draug
rem
o
vi
n
g
Bio::FeatureIO a
n
d
Bio:
:
SeqFea
t
u
re:
:
Annota
t
ed
.
.
.
commit
|
commitdiff
|
tree
2013-02-06
Carnë Drau
g
maint: mention
r
ecent
changes to Bio::SeqIO::fas
t
a
commit
|
commitdiff
|
tree
2013-02-06
Car
n
ë
Draug
Bio::SeqIO::fasta - remove package vari
a
ble
s
for defa
u
lts
commit
|
commitdiff
|
tree
2013-02-05
C
a
rn
ë
Dr
a
ug
Bio::SeqIO::fasta
- implement block
m
e
t
hod for pretty
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
C
arn
ë
D
ra
u
g
f
ollow perl r
e
comm
e
n
d
a
t
ions
:
commit
|
commitdiff
|
tree
2013-01-28
C
a
r
n
ë Draug
fin
i
sh moving the
B
io-D
B
-EUti
l
ities to the Bio-EUtilities
.
.
.
commit
|
commitdiff
|
tree
2013-01-28
Carn
ë
Draug
Fi
x
ing
POD d
o
c
umenta
t
ion
.
Em
p
ty line befor
e
=
cut to
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Car
n
ë
Draug
genbank_r
e
f_e
x
t
ractor: move 'require's to Ge
t
Options
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Ca
r
në Draug
g
enban
k
_re
f
_
e
xtractor:
changed defau
l
t
a
s
semb
l
y regex
commit
|
commitdiff
|
tree
2011-09-28
Carnë Draug
gen
b
ank_ref
_
e
x
tractor: small typo
on documentation
commit
|
commitdiff
|
tree
2011-09-28
Ca
r
n
ë
D
raug
genbank_ref_extractor: added assembly
to exported data
commit
|
commitdiff
|
tree
2011-09-22
C
arnë Draug
genbank_
r
ef_extractor: typo on all instances of var
.
.
.
commit
|
commitdiff
|
tree
2011-09-22
Carnë Draug
genbank_ref_extractor
:
small f
i
xes on P
O
D doc
u
me
n
t
a
tion
commit
|
commitdiff
|
tree
2011-09-21
Carnë Draug
genb
a
nk
_
r
e
f
_
extractor
:
new script t
o
make sear
c
h on
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
Ca
r
në D
r
a
ug
Fix bug when using ST
D
OUT
or
w
riting to
f
i
le withou
t
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
Carnë
Draug
I
m
p
rovemen
t
s to POD
commit
|
commitdiff
|
tree
2011-07-25
Carnë
D
raug
r
e
placed i
d
enta
t
ion t
a
bs for spac
e
s
commit
|
commitdiff
|
tree
2011-07-25
Car
n
ë Dra
u
g
Don't mess with $^W
.
Control with w
a
r
ni
n
g
s
pragma instead
commit
|
commitdiff
|
tree
2011-07-25
C
arnë Draug
s
c
rip
t
s: added 'u
s
e warni
n
gs' to all scripts without it
commit
|
commitdiff
|
tree
2011-07-25
Carn
ë
Draug
scripts: replaced -w switch
b
y
use warnings
commit
|
commitdiff
|
tree
2011-07-20
Carnë Draug
Script
documentation
f
ix to match their n
a
mes with
.
.
.
commit
|
commitdiff
|
tree
2011-07-19
Carnë D
r
aug
Renamed all
script
s
with prf
i
x bp_
commit
|
commitdiff
|
tree