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Removal of Bio::Tools::Phylo::PAML.pm and related modules, tests, and docs
2017-09-08
C
a
rnë Draug
Remov
a
l
o
f Bi
o
::Too
l
s::
P
hylo:
:
P
A
ML
.
p
m
and relat
e
d modules
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Carnë
D
rau
g
Bio::
P
hyloNetw
o
rk
:
:muVecto
r
: revert non-
t
ypo
f
rom 54c99cf411
commit
|
commitdiff
|
tree
2017-08-30
Carnë Draug
m
aint: fix multiple typos
i
dentified by
l
intian
commit
|
commitdiff
|
tree
2015-11-29
Car
n
ë Draug
bp_pairw
i
se_
k
aks
.
pl: do
n
ot
mix space and tabs for
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
C
arnë Draug
Bio::
A
lign::Utilities
- remo
v
e
usa
g
e of /r option to
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Drau
g
Fix nonsens
e
in co
d
e c
o
mments
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Bio::Alig
n
::Utilities - follow som
e
perl best
p
ractic
e
s
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Bio::Align::Utilities - new
f
unctio
n
most_
c
o
m
mon_s
e
que
n
ces
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Bio:
:
SimpleAlign - follow som
e
per
l
best practices
commit
|
commitdiff
|
tree
2013-04-04
Carnë Drau
g
maint: remove files that have been moved to a s
e
p
arate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carn
ë
Draug
maint:
u
pdate Chang
e
s after removing fil
e
s from
B
io
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Draug
m
ain
t
: remo
v
e files that
have been m
o
ve
d
to a separate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Ca
r
në Draug
tests: mov
e
tests from Roo
t
to Assembly
a
n
d SeqIO
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carn
ë
Draug
m
aint
:
remove hard
t
a
bs and trailing whi
t
espace
commit
|
commitdiff
|
tree
2013-03-28
Ca
r
në
D
raug
tests for i
n
heritance should belong
on the child class
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Ca
r
në Drau
g
remove
h
ard tabs
a
nd
tr
a
i
l
ing whites
p
ace
f
rom some
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë Dr
a
ug
Annotation: fi
x
typo on test
commit
|
commitdiff
|
tree
2013-03-26
C
a
rnë
Dr
a
ug
B
io:
:
Cl
u
ster::Se
q
uen
c
eFam
i
ly - bug fi
x
es and
p
erforman
c
e
commit
|
commitdiff
|
tree
2013-03-26
Carnë
D
raug
doc: f
i
x ind
e
ntatio
n
, remove
ha
r
d
tab
s
a
n
d
trail
i
ng
.
.
.
commit
|
commitdiff
|
tree
2013-03-21
Carnë Draug
r
ecover GenericWebAgent
f
rom Bio-EUtiliti
e
s
commit
|
commitdiff
|
tree
2013-03-13
Carnë Draug
split
B
io
-
Biblio
in
t
o a
s
ep
a
rate dis
t
ribution
commit
|
commitdiff
|
tree
2013-03-12
Carnë Draug
Me
r
ge p
u
ll request #53 from bvaisvil
/
master
commit
|
commitdiff
|
tree
2013-03-06
Carn
ë
D
r
a
ug
Bio::Perl - fix indentation (re
m
ove
tabs, and weird
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Ca
r
në Draug
Don't use a
separ
a
te default scalar whe
n
th
e
re's a
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Carn
ë
Draug
f
o
llo
w
p
erl recommen
d
a
t
io
n
s
:
commit
|
commitdiff
|
tree
2013-03-04
C
arnë D
r
aug
fix inde
n
tation (remove ta
b
s, and
w
eird 3
spa
c
es indentation
)
commit
|
commitdiff
|
tree
2013-03-04
Carnë Draug
follow perl recommendations:
commit
|
commitdiff
|
tree
2013-03-04
Carnë Drau
g
use until in
s
te
a
d of while(1){last if
.
.
.
}
commit
|
commitdiff
|
tree
2013-03-04
Carnë D
r
aug
fix indentation (remove t
a
b
s, 3 space and 2 space ind
e
n
t
a
t
ion)
commit
|
commitdiff
|
tree
2013-02-11
C
a
rn
ë
Draug
rem
o
ving
Bio
:
:FeatureIO and B
i
o::S
e
qFeature
:
:Annotated
.
.
.
commit
|
commitdiff
|
tree
2013-02-06
Carnë
D
raug
maint
:
mention rece
n
t changes
t
o Bio
:
:SeqIO::fasta
commit
|
commitdiff
|
tree
2013-02-06
C
arnë Draug
Bio::SeqIO::fasta - re
m
ove pack
a
ge
v
a
r
iable
s
for defaults
commit
|
commitdiff
|
tree
2013-02-05
Carnë Draug
Bi
o
::S
e
q
IO::fas
t
a - implement block method f
o
r p
r
et
t
y
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Carnë
Draug
follow
perl recommendations:
commit
|
commitdiff
|
tree
2013-01-28
Car
n
ë Dra
u
g
f
inish movin
g
the Bio-DB-EUtilities
to th
e
Bio-EUtili
t
i
e
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-28
Carnë Dra
u
g
Fix
i
ng
POD
docu
m
entatio
n
.
E
mpty
l
i
ne b
e
for
e
=cu
t
to
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Carn
ë
Draug
genb
a
nk
_
re
f
_ex
t
ractor
:
move 'require's to GetOptions
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Ca
r
në Draug
genbank_ref_extr
a
ct
o
r:
ch
a
ng
e
d
defaul
t
assembly
r
e
g
ex
commit
|
commitdiff
|
tree
2011-09-28
Carnë
D
raug
genbank_re
f
_e
x
tract
o
r: sm
a
ll ty
p
o on documentation
commit
|
commitdiff
|
tree
2011-09-28
Carnë
Draug
g
en
b
ank_ref_ext
r
actor: added assembly to exported da
t
a
commit
|
commitdiff
|
tree
2011-09-22
Carnë Drau
g
g
enbank_ref_extractor: t
y
po on
a
l
l in
s
tances of var
.
.
.
commit
|
commitdiff
|
tree
2011-09-22
Car
n
ë
Dra
u
g
genb
a
nk_re
f
_extractor
:
sm
a
ll fixes on POD doc
u
mentation
commit
|
commitdiff
|
tree
2011-09-21
C
a
rnë Draug
g
e
nbank_ref_extr
a
cto
r
: new script
to make
sea
r
ch on
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
Carnë Draug
Fix
bug whe
n
using STDOUT or writing
t
o
file withou
t
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
C
arnë Draug
Im
p
rovements to POD
commit
|
commitdiff
|
tree
2011-07-25
Carnë Draug
r
e
placed identation tab
s
f
or
s
paces
commit
|
commitdiff
|
tree
2011-07-25
Ca
r
në Draug
D
o
n't mess with
$
^
W
.
Control with warnings pragma instead
commit
|
commitdiff
|
tree
2011-07-25
Carnë
Draug
scripts: a
d
ded 'use warnings' to
all scripts without
i
t
commit
|
commitdiff
|
tree
2011-07-25
Carnë
Dr
a
u
g
s
c
ripts: replaced
-
w sw
i
tch by use wa
r
nings
commit
|
commitdiff
|
tree
2011-07-20
Carnë Draug
Script doc
u
men
t
ation fix to match th
e
ir names with
.
.
.
commit
|
commitdiff
|
tree
2011-07-19
Carnë Dr
a
ug
Renamed all
s
cripts with prfix bp_
commit
|
commitdiff
|
tree