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Removal of Bio::Tools::Phylo::PAML.pm and related modules, tests, and docs
2017-09-08
Carn
ë
Draug
Removal of Bio::
T
ools::Phylo::PAML
.
pm and related modules
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Carnë Draug
Bio::PhyloNetw
o
rk::muVect
o
r: revert non-typo from 54c99cf4
1
1
commit
|
commitdiff
|
tree
2017-08-30
Carnë Draug
m
a
int: f
i
x mult
i
ple ty
p
os id
e
ntified by l
i
nt
i
a
n
commit
|
commitdiff
|
tree
2015-11-29
C
arnë Dr
a
ug
bp_pairwise_kaks
.
pl: do not mix space and
t
a
b
s
f
or
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Bio::Align::Ut
i
l
ities - rem
o
ve usa
g
e of /r optio
n
to
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Drau
g
Fix
nonsense
in
c
ode comments
.
commit
|
commitdiff
|
tree
2013-11-26
Ca
r
n
ë
Draug
Bio::
A
lign
:
:Utiliti
e
s - fol
l
ow som
e
pe
r
l
best pra
c
tice
s
.
commit
|
commitdiff
|
tree
2013-11-26
Car
n
ë
Draug
Bio::A
l
i
g
n
::
U
t
i
l
i
ties
-
new function m
o
st_common_sequences
commit
|
commitdiff
|
tree
2013-11-26
Car
n
ë Draug
B
io::Simple
A
li
g
n - follow some perl
b
est
p
ract
i
ces
commit
|
commitdiff
|
tree
2013-04-04
Carnë D
r
aug
mai
n
t: rem
o
ve files that
have been moved to a separate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carn
ë
Draug
m
a
int
:
update Changes after removin
g
files from Bio
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Draug
mai
n
t
: remove
files that have been
m
oved to a s
e
par
a
te
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Dr
a
ug
t
e
st
s
: move tests from Root to
Assembly an
d
S
eqI
O
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Ca
r
në D
r
aug
m
a
in
t
: re
m
ov
e
h
ard
t
ab
s
and trailing whitespace
commit
|
commitdiff
|
tree
2013-03-28
C
a
rnë Draug
t
e
s
ts
for inheritance should
belong on the
child clas
s
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë Draug
remove
h
ard tabs and trailing whitespace from s
o
m
e
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë Drau
g
A
n
notation: fix typo on tes
t
commit
|
commitdiff
|
tree
2013-03-26
Carn
ë
Draug
B
i
o::C
l
uste
r
::SequenceFamily - bug fixes
and pe
r
forma
n
ce
commit
|
commitdiff
|
tree
2013-03-26
Carnë
Draug
doc: fix indentatio
n
, remove hard tabs and tra
i
l
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2013-03-21
Carnë Draug
recover GenericWebAgent fro
m
B
io-EU
t
il
i
ti
e
s
commit
|
commitdiff
|
tree
2013-03-13
Carnë Draug
split Bio-Bibli
o
into
a
s
ep
a
rate
d
ist
r
ibution
commit
|
commitdiff
|
tree
2013-03-12
Carnë D
r
aug
Merge pull re
q
uest
#
53 from bvaisvil/
m
aster
commit
|
commitdiff
|
tree
2013-03-06
Carnë
Draug
B
io::P
e
rl - fix
i
nden
t
at
i
on
(
remove ta
b
s
, and w
e
i
r
d
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Car
n
ë
D
raug
Don't us
e
a sep
a
rate de
f
ault s
c
a
l
ar when th
e
re's a
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Carnë
D
raug
f
o
ll
o
w p
e
rl recommend
a
t
i
o
ns:
commit
|
commitdiff
|
tree
2013-03-04
Carnë Draug
fi
x
i
ndentati
o
n (remove
t
abs, and we
i
rd 3
s
p
a
ces indentatio
n
)
commit
|
commitdiff
|
tree
2013-03-04
Carnë
Dr
a
ug
follow p
e
rl recom
m
en
d
ations
:
commit
|
commitdiff
|
tree
2013-03-04
Carnë Draug
use u
n
til
instead o
f
wh
i
le(1){last if
.
.
.
}
commit
|
commitdiff
|
tree
2013-03-04
Car
n
ë Dra
u
g
fix in
d
e
n
ta
t
ion
(remove ta
b
s, 3 space and 2 space inden
t
ation)
commit
|
commitdiff
|
tree
2013-02-11
Carnë Draug
rem
o
vin
g
Bio::Featur
e
IO and
B
io::SeqFeature::Annotated
.
.
.
commit
|
commitdiff
|
tree
2013-02-06
Ca
r
n
ë
Draug
maint: menti
o
n
re
c
ent c
h
anges to
B
io::SeqIO::fast
a
commit
|
commitdiff
|
tree
2013-02-06
C
arnë
D
ra
u
g
Bio:
:
S
e
q
I
O::
f
asta - remove packag
e
variables for
d
e
faults
commit
|
commitdiff
|
tree
2013-02-05
C
a
rnë Draug
Bio::SeqI
O
::fasta
-
implement block
met
h
od for p
r
etty
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Carn
ë
Draug
follow perl recomm
e
nd
a
tions:
commit
|
commitdiff
|
tree
2013-01-28
Ca
r
në Dr
a
ug
finish moving the Bio-DB-EUtilities to t
h
e Bio-EUtilities
.
.
.
commit
|
commitdiff
|
tree
2013-01-28
Carn
ë
Draug
Fixing POD documentation
.
Empty line before
=cut to
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Carnë Dra
u
g
ge
n
bank_ref_extrac
t
or: move 'requir
e
's to Get
O
pti
o
ns
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Carn
ë
Dra
u
g
genbank_r
e
f
_
ex
t
r
ac
t
or: ch
a
n
ged d
e
fau
l
t assembly regex
commit
|
commitdiff
|
tree
2011-09-28
Ca
r
në Dr
a
ug
gen
b
ank_ref_
e
x
t
ractor: sma
l
l typo o
n
docum
e
ntation
commit
|
commitdiff
|
tree
2011-09-28
Carnë Draug
genbank
_
r
ef_extractor: added assembly to exporte
d
d
a
ta
commit
|
commitdiff
|
tree
2011-09-22
Carn
ë
Draug
g
enbank_ref_extr
a
ct
o
r: typ
o
o
n all in
s
t
ances of var
.
.
.
commit
|
commitdiff
|
tree
2011-09-22
Car
n
ë Dr
a
ug
genbank_re
f
_extra
c
tor: s
m
all fixes o
n
POD document
a
t
ion
commit
|
commitdiff
|
tree
2011-09-21
Carnë Draug
genba
n
k_ref_extractor: new scri
p
t to make sea
r
c
h
o
n
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
Carnë Draug
F
ix bug
w
h
e
n using STDOUT or writing to file without
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
C
a
rn
ë
Draug
I
m
provements to POD
commit
|
commitdiff
|
tree
2011-07-25
Carnë Draug
replaced identation tabs for spaces
commit
|
commitdiff
|
tree
2011-07-25
Ca
r
n
ë
Draug
Don't m
e
s
s with
$
^W
.
C
on
t
r
ol wi
t
h warnings
p
ragma inst
e
ad
commit
|
commitdiff
|
tree
2011-07-25
Carnë
Draug
scripts: added 'us
e
warnings' to all scripts without it
commit
|
commitdiff
|
tree
2011-07-25
C
arnë
D
raug
s
c
ripts: replaced -w
s
wi
t
ch
by use war
n
in
g
s
commit
|
commitdiff
|
tree
2011-07-20
Carnë
Draug
Script docu
m
enta
t
ion fix to match their names with
.
.
.
commit
|
commitdiff
|
tree
2011-07-19
C
a
rnë D
r
aug
Renamed al
l
scrip
t
s
with p
r
fix bp
_
commit
|
commitdiff
|
tree