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Removal of Bio::Tools::Phylo::PAML.pm and related modules, tests, and docs
2017-09-08
Carnë D
r
aug
Remova
l
of Bio::Tools::Phylo::PAML
.
pm and related modules
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Carnë Draug
Bio
:
:Phyl
o
Network:
:
muVe
c
tor: revert no
n
-typ
o
f
rom
5
4c99c
f
4
11
commit
|
commitdiff
|
tree
2017-08-30
Carnë Dr
a
ug
maint: fix multiple typos
i
dentified by lintian
commit
|
commitdiff
|
tree
2015-11-29
Carnë Draug
b
p_pairwise_kaks
.
p
l
: do not mix spac
e
a
nd
t
abs for
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
B
io::Align
:
:
U
t
ilities - remove us
a
g
e of /r option to
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Fix nonse
n
se in code
c
omm
e
n
t
s
.
commit
|
commitdiff
|
tree
2013-11-26
Ca
r
n
ë Draug
Bio::Align
:
:Utilities - follow
some perl best pr
a
c
tices
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Drau
g
Bio::Al
i
gn::Util
i
ties - new func
t
i
on
m
ost_common_seque
n
ces
commit
|
commitdiff
|
tree
2013-11-26
Carn
ë
D
rau
g
Bio
:
:SimpleAl
i
gn - follow
s
ome perl best practices
commit
|
commitdiff
|
tree
2013-04-04
Carnë Dra
u
g
mai
n
t: remove
f
il
e
s
that hav
e
been mo
v
e
d
t
o
a separate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
C
arnë Draug
mai
n
t: up
d
a
te Cha
n
ges after
removing files from Bio
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Draug
maint: remove
file
s
that have b
e
e
n
mo
v
ed to
a sep
a
rate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Draug
te
s
ts: move tes
t
s
from Root
t
o Assembly an
d
SeqIO
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carn
ë
Draug
maint: remove h
a
rd tabs and t
r
a
iling wh
i
tes
p
ace
commit
|
commitdiff
|
tree
2013-03-28
Carnë Draug
tests for
inheritance
should belong o
n
t
h
e child class
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë D
r
a
ug
remove hard
t
abs and trailing
w
hitespac
e
from som
e
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Car
n
ë Draug
Annotat
i
on:
fix
ty
p
o o
n
test
commit
|
commitdiff
|
tree
2013-03-26
Carnë
Draug
Bio::
C
l
uste
r
::Seque
n
ceFamily - bu
g
fixes and perf
o
r
ma
n
ce
commit
|
commitdiff
|
tree
2013-03-26
C
arnë D
r
aug
doc: fi
x
in
d
entation,
r
emove hard tabs and trailing
.
.
.
commit
|
commitdiff
|
tree
2013-03-21
Carnë Draug
recover
G
en
e
ricWe
b
Agent from B
i
o
-
E
U
tilities
commit
|
commitdiff
|
tree
2013-03-13
Car
n
ë D
r
aug
split
Bio-Bi
b
lio int
o
a separ
a
te distribution
commit
|
commitdiff
|
tree
2013-03-12
Carnë
D
rau
g
Merge pull
reques
t
#53 from bvaisvil/master
commit
|
commitdiff
|
tree
2013-03-06
C
a
rnë Draug
Bio::Perl
- fix
inde
n
tation (remove
t
a
b
s, and we
i
rd
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Carnë Dr
a
ug
Don't use a s
e
parate default sca
l
ar when
t
h
ere
'
s a
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Carnë
Draug
follo
w
p
e
rl
re
c
ommendations:
commit
|
commitdiff
|
tree
2013-03-04
Ca
r
në Draug
fix indentation (
r
emove tab
s
, and
we
i
r
d
3 spaces indentatio
n
)
commit
|
commitdiff
|
tree
2013-03-04
Carnë Draug
follow perl recomm
e
ndations:
commit
|
commitdiff
|
tree
2013-03-04
Carnë Dr
a
ug
u
s
e
unt
i
l
instead of
whi
l
e(1){last if
.
.
.
}
commit
|
commitdiff
|
tree
2013-03-04
Carn
ë
Dra
u
g
fix
indentation (re
m
ove ta
b
s, 3 sp
a
ce
a
nd
2
sp
a
ce indentation)
commit
|
commitdiff
|
tree
2013-02-11
Carnë Draug
removing B
i
o::Featur
e
IO and Bio::SeqFeature::An
n
otated
.
.
.
commit
|
commitdiff
|
tree
2013-02-06
Car
n
ë Draug
maint: mention recent change
s
t
o
Bi
o
::SeqIO::
f
asta
commit
|
commitdiff
|
tree
2013-02-06
Carn
ë
D
raug
Bio::SeqIO::fasta -
r
e
m
ove p
a
ckag
e
variables for defaults
commit
|
commitdiff
|
tree
2013-02-05
Carnë Draug
Bio::
S
eqI
O
::fasta - implement b
l
o
ck metho
d
for pretty
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Carnë
D
ra
u
g
fol
l
ow perl r
e
commenda
t
io
n
s:
commit
|
commitdiff
|
tree
2013-01-28
Carnë Draug
finis
h
movin
g
the Bio-DB
-
EUtilitie
s
to the B
i
o
-
EUtilitie
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-28
Carnë Draug
Fixing POD docu
m
entat
i
on
.
Empty line befo
r
e =cut to
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Car
n
ë
D
raug
genba
n
k_re
f
_extractor: move 'require's to GetOptions
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Carnë
Dra
u
g
g
e
nbank_ref_
e
xtractor: chan
g
e
d
default assembly rege
x
commit
|
commitdiff
|
tree
2011-09-28
Carnë Drau
g
genbank_ref_extractor: small ty
p
o on documenta
t
ion
commit
|
commitdiff
|
tree
2011-09-28
C
arn
ë
Draug
genb
a
nk_ref_ext
r
actor: add
e
d asse
m
bly to expor
t
e
d d
a
ta
commit
|
commitdiff
|
tree
2011-09-22
Carnë
Draug
g
e
n
bank_ref_extractor: typo on all inst
a
nces of var
.
.
.
commit
|
commitdiff
|
tree
2011-09-22
C
a
rnë Dra
u
g
genbank_r
e
f_ex
t
ractor: small fix
e
s
o
n POD d
o
c
u
me
n
tation
commit
|
commitdiff
|
tree
2011-09-21
Carnë Draug
g
e
nbank_ref_ext
r
actor: n
e
w
s
c
ript to make s
e
arch o
n
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
Carnë Dra
u
g
F
ix bug w
h
e
n
u
s
i
ng STDOUT
or writing
t
o f
i
le without
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
Carnë D
r
aug
Improvements to P
O
D
commit
|
commitdiff
|
tree
2011-07-25
Carn
ë
D
r
aug
repla
c
ed identatio
n
tabs
f
or sp
a
ces
commit
|
commitdiff
|
tree
2011-07-25
Carnë Draug
D
on't mess with $^W
.
Con
t
ro
l
with
warnin
g
s
pragma inste
a
d
commit
|
commitdiff
|
tree
2011-07-25
Carnë Dr
a
u
g
scripts: added 'use warnings' to all scripts without it
commit
|
commitdiff
|
tree
2011-07-25
Carnë Draug
scripts:
re
p
la
c
ed -w switch by use
warni
n
g
s
commit
|
commitdiff
|
tree
2011-07-20
Carnë Dra
u
g
Sc
r
i
p
t
d
ocu
m
e
ntatio
n
fix t
o
m
a
t
ch th
e
ir na
m
es with
.
.
.
commit
|
commitdiff
|
tree
2011-07-19
Carnë
Draug
Renamed all
s
cripts with
prfix
bp_
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|
commitdiff
|
tree