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Bio::Tools::CodonTable and Bio::Tools::IUPAC: use our and drop BEGIN blocks.
2018-09-14
Carnë Draug
Remo
v
e AlignIO and Index stockholm module
s
t
o new
B
io
.
.
.
commit
|
commitdiff
|
tree
2018-09-14
Car
n
ë Draug
Bi
o
::DB::Universal: m
o
v
e into its own distributio
n
commit
|
commitdiff
|
tree
2018-09-14
Carn
ë
Draug
m
aint: simplify README to cover simple
i
nst
a
ll in
s
tructions
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
B
ring base classes fr
o
m BioPerl-run back to BioPerl
.
commit
|
commitdiff
|
tree
2018-09-13
Ca
r
n
ë Draug
Remove use
o
f Bio::Perl
w
hich
h
as b
e
e
n
moved to
B
i
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë D
r
a
u
g
Bio::DB::MeSH move to its own
distri
b
ution
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Drau
g
Mov
e
HMMER r
e
late
d
modules, test
s
, and
p
rograms
to
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
B
i
o::DB::
T
F
BS na
m
espace
has been
m
o
ved t
o
its own distributi
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Bio::DB::H
I
V
a
nd related modu
l
es an
d
scripts moved
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë D
r
aug
Bio::Align::Graphics
:
mo
v
e into its own distribution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
C
a
rnë Dr
a
ug
Bi
o
:
:Tools:
:
R
u
n::RemoteBlast: m
o
ve into a new distribution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bio::Perl: mo
v
e its
o
w
n
distribu
t
ion named B
i
o
-
Proced
u
ral
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bio::MolEvol::CodonMo
d
el
:
move
i
nto it separ
a
t
e
r
e
po
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë
Draug
Bio::
S
eq
I
O
::entrezg
e
n
e
:
move to exist
i
n
g
B
io-ASN1-entrezg
e
ne
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë D
r
aug
Bio/Restriction/*: m
o
ve to
another r
e
po
with
same name
.
commit
|
commitdiff
|
tree
2018-09-11
Car
n
ë D
r
a
u
g
Bio/Tools/Gel
.
pm: mo
v
e
t
o another repo with same
n
ame
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/SeqEv
o
l
u
tion/*:
m
ove to anoth
e
r
r
epo with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
arnë Dra
u
g
Bio/Structure/*: move to another r
e
p
o
with
s
ame name
.
commit
|
commitdiff
|
tree
2018-09-11
Carn
ë
Dr
a
ug
t/data: remove more test data files which moved t
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Dr
a
ug
Bio/Assembly*: move to a
n
other
r
e
p
o
w
ith same name
.
commit
|
commitdiff
|
tree
2018-09-11
C
a
r
në Draug
Bio/PhyloNetwork*: move
to anot
h
er
r
epo with same name
.
commit
|
commitdiff
|
tree
2018-09-11
C
a
rnë
D
raug
B
io/SeqIO/exc
e
l
.
p
m
:
move to another re
p
o with s
a
m
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
a
r
në Dr
a
ug
Bio/T
r
e
e
IO/svggraph
.
pm: mo
v
e to
anot
h
er
repo with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Bio
/
Tree/Draw/Cladogram
.
pm:
m
ove to another re
p
o
w
ith
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Car
n
ë
D
raug
B
i
o/Draw/
P
ictogr
a
m
.
pm: move to another repo with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Move all
m
odules interfacin
g
to A
C
eDB servers to a
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Mo
v
e
all N
e
X
M
L relate
d
modules
and tests
t
o
a
new
Bi
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
R
emove so
m
e unused test da
t
a files
.
commit
|
commitdiff
|
tree
2018-09-10
C
arnë Draug
Remove entire Bio::PopGen namespace and relat
e
d
m
odules
.
.
.
commit
|
commitdiff
|
tree
2018-09-08
C
a
rnë Draug
scripts/tree/bp_blast
2
tree
.
pl: mo
v
ed to bi
o
perl-run
commit
|
commitdiff
|
tree
2018-09-07
Ca
r
në
Dr
a
u
g
de
o
bfuscator: remove this wh
o
l
e
project
commit
|
commitdiff
|
tree
2018-09-04
Carnë Draug
Con
s
istent shebang lin
e
to '+#!/us
r
/b
i
n/
p
erl'
commit
|
commitdiff
|
tree
2018-08-23
Carnë Draug
deobfuscator
s
cripts: use warnings pragma instead of
.
.
.
commit
|
commitdiff
|
tree
2018-07-25
Carnë Draug
Bio::MolEvol::Codon
M
odel: fix do
c
umentation (issue
.
.
.
commit
|
commitdiff
|
tree
2017-09-13
C
a
rn
ë
D
r
a
ug
example
s
/align
/
c
l
ustal
w
.
pl
:
remove fi
l
e
,
no
w
part of
.
.
.
commit
|
commitdiff
|
tree
2017-09-08
Carnë Draug
Removal of Bio::Tools:
:
Phylo::PAML
.
p
m and re
l
ated modul
e
s
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Carnë D
r
aug
Bi
o
:
:Phylo
N
etwork
:
:mu
V
e
c
to
r
: reve
r
t
non-typo from 54c99
c
f411
commit
|
commitdiff
|
tree
2017-08-30
Carn
ë
Dr
a
ug
maint
:
fix multiple typos ident
i
fied by
lintian
commit
|
commitdiff
|
tree
2015-11-29
Car
n
ë Draug
b
p_p
a
ir
w
ise
_
kaks
.
pl: do not m
i
x
s
p
a
ce
a
nd tabs for
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë D
r
aug
B
i
o::Align
:
:Utilities - r
e
move u
s
age of
/r opt
i
on t
o
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Ca
r
në Draug
Fix nonsense
i
n code
comments
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Bio::Align
:
:Utilities
-
follo
w
s
ome perl best practic
e
s
.
commit
|
commitdiff
|
tree
2013-11-26
Car
n
ë
D
ra
u
g
Bio:
:
Align::U
t
ilities - new function mo
s
t_common_sequences
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Bio::Si
m
pleAlign - follow so
m
e
perl b
e
s
t practices
commit
|
commitdiff
|
tree
2013-04-04
Carn
ë
Draug
main
t
: remov
e
f
iles that have been
moved to a se
p
ar
a
te
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
C
arnë Draug
m
a
int
:
update C
h
anges afte
r
removing files from
B
io
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Draug
maint:
r
emove files tha
t
have b
e
en m
o
v
e
d to
a separate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Draug
test
s
:
m
ov
e
t
e
sts f
r
om Root to Assembl
y
and SeqIO
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë
D
raug
maint: re
m
o
v
e
h
ard tab
s
and trailing
whitesp
a
c
e
commit
|
commitdiff
|
tree
2013-03-28
Carnë Draug
t
e
s
ts for inheritance should
b
elong on
t
h
e chil
d
c
l
as
s
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Car
n
ë Draug
remove
hard tabs
a
nd trai
l
ing
white
s
pace from some
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
C
a
r
në Draug
Annotation: f
i
x typo on test
commit
|
commitdiff
|
tree
2013-03-26
Carnë Drau
g
Bio
:
:Cluster:
:
Seque
n
ceFamily - bug fixes and perf
o
rmance
commit
|
commitdiff
|
tree
2013-03-26
Carnë Draug
doc:
f
ix ind
e
n
t
a
t
ion, remove hard
tabs and trailing
.
.
.
commit
|
commitdiff
|
tree
2013-03-21
Car
n
ë
Drau
g
rec
o
ver GenericWebAg
e
nt fr
o
m
B
io-EUtilities
commit
|
commitdiff
|
tree
2013-03-13
Carnë D
r
aug
s
plit Bio-Bib
l
io into a separate distribution
commit
|
commitdiff
|
tree
2013-03-12
C
a
rnë Dra
u
g
Merge pull request #53 from
b
vaisvil/master
commit
|
commitdiff
|
tree
2013-03-06
Carnë D
r
aug
Bi
o
::Perl - f
i
x
indentation (remove tabs,
a
nd weird
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
C
a
r
n
ë Draug
D
on't use a
s
e
p
a
rate default scalar
when there's a
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Carn
ë
Draug
f
ollow perl recommen
d
ati
o
ns:
commit
|
commitdiff
|
tree
2013-03-04
Ca
r
në D
r
aug
f
ix inden
t
ation (remove tabs, and weird
3
spac
e
s
i
ndent
a
tion)
commit
|
commitdiff
|
tree
2013-03-04
Ca
r
në Draug
follow perl
recom
m
end
a
tions:
commit
|
commitdiff
|
tree
2013-03-04
C
a
rnë Draug
use until instead
of while(1
)
{last if
.
.
.
}
commit
|
commitdiff
|
tree
2013-03-04
Carnë
Dr
a
ug
fix inde
n
tation (remove tabs,
3
spa
c
e and 2
space i
n
dentation)
commit
|
commitdiff
|
tree
2013-02-11
Carnë
Draug
removing Bio::FeatureIO
a
nd Bio
:
:SeqFeature::Annotated
.
.
.
commit
|
commitdiff
|
tree
2013-02-06
Car
n
ë Dr
a
u
g
maint: mention recent cha
n
g
e
s to Bio::SeqIO::fasta
commit
|
commitdiff
|
tree
2013-02-06
Carnë Draug
Bio:
:
SeqIO
:
:fasta - re
m
ove package v
a
ri
a
bles for
de
f
aults
commit
|
commitdiff
|
tree
2013-02-05
C
a
r
në Dra
u
g
B
io::
S
eqIO:
:
fasta
- implement block method for p
r
etty
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Ca
r
në Dra
u
g
follow perl
recommendations:
commit
|
commitdiff
|
tree
2013-01-28
Carnë
Draug
fin
i
s
h
moving
t
he
B
io-DB-EUt
i
liti
e
s to the
Bio-EUtilities
.
.
.
commit
|
commitdiff
|
tree
2013-01-28
Carnë Draug
F
i
xing PO
D
documentation
.
E
m
p
ty
l
ine before =cut
to
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
C
arnë Draug
ge
n
b
ank_ref_extrac
t
or: move 'require's to GetOp
t
i
ons
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Carnë D
r
aug
genbank_ref_extractor: changed default assembly regex
commit
|
commitdiff
|
tree
2011-09-28
Carnë Drau
g
genbank_ref_extractor: small ty
p
o on documen
t
ation
commit
|
commitdiff
|
tree
2011-09-28
Carnë D
r
au
g
genb
a
nk
_
ref_extractor: adde
d
a
s
se
m
b
l
y to
exported d
a
ta
commit
|
commitdiff
|
tree
2011-09-22
Carnë Draug
g
enb
a
n
k
_ref_extrac
t
or: t
y
po o
n
all in
s
tances of v
a
r
.
.
.
commit
|
commitdiff
|
tree
2011-09-22
Carnë Draug
genbank_ref_ext
r
actor: small fixe
s
on POD documenta
t
ion
commit
|
commitdiff
|
tree
2011-09-21
Ca
r
n
ë D
r
aug
genbank_re
f
_extractor: new
scri
p
t to m
a
ke search on
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
Carnë Dr
a
ug
Fix bug
when
u
s
i
ng STDOUT or writing to file wi
t
hout
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
C
a
r
n
ë
Draug
I
m
provements to POD
commit
|
commitdiff
|
tree
2011-07-25
Carnë Dra
u
g
repl
a
ce
d
identation tabs for sp
a
ces
commit
|
commitdiff
|
tree
2011-07-25
Carnë Draug
Don
'
t mess with
$
^
W
.
Control
with war
n
ings pragma instead
commit
|
commitdiff
|
tree
2011-07-25
Carnë Draug
s
c
ripts: added 'use warnings' t
o
all
scripts without
it
commit
|
commitdiff
|
tree
2011-07-25
Carnë Draug
scripts: repla
c
ed -w
s
w
itch by
u
s
e
warnings
commit
|
commitdiff
|
tree
2011-07-20
Carnë Draug
Script document
a
tion
f
ix to
m
atch
t
heir names with
.
.
.
commit
|
commitdiff
|
tree
2011-07-19
Carnë Draug
Renamed all scripts with
p
rfix b
p
_
commit
|
commitdiff
|
tree