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let alpha be more free - don't try and restrict it
2002-11-10
j
a
son
skip if ret v
a
l is 0
commit
|
commitdiff
|
tree
2002-11-10
jason
consistency
commit
|
commitdiff
|
tree
2002-11-10
jason
code beautification
commit
|
commitdiff
|
tree
2002-11-10
j
a
s
o
n
p
l
a
tform i
n
dependent filename
commit
|
commitdiff
|
tree
2002-11-09
jason
respect the original
cwd
commit
|
commitdiff
|
tree
2002-09-18
jason
synopsis doc
commit
|
commitdiff
|
tree
2002-09-18
ja
s
on
de
f
ault should be F3X4
commit
|
commitdiff
|
tree
2002-09-18
jason
Matt
h
ew's Ch
a
nges comm
i
t
t
ed: Add support t
o
save_output
.
.
.
commit
|
commitdiff
|
tree
2002-09-18
jason
handle exe apps
commit
|
commitdiff
|
tree
2002-09-05
ja
s
on
SAX/
S
ax ->
PerlSAX
commit
|
commitdiff
|
tree
2002-08-14
jason
for building
manifest
commit
|
commitdiff
|
tree
2002-08-14
jason
c
o
smet
i
c c
o
de fi
x
commit
|
commitdiff
|
tree
2002-08-14
jason
de
s
cribe
t
he
current
sta
t
e of a
f
fair
commit
|
commitdiff
|
tree
2002-07-30
j
ason
skip t
e
sts
commit
|
commitdiff
|
tree
2002-07-29
ja
s
on
test file for
TCoffee
commit
|
commitdiff
|
tree
2002-07-29
j
a
s
on
w
h
o
o
ps,one mo
r
e time
,
cle
a
nup tempfiles
a
nd
d
irs
commit
|
commitdiff
|
tree
2002-07-29
jaso
n
cleanup of tem
p
files works
commit
|
commitdiff
|
tree
2002-07-29
ja
s
on
handle
b
ad res
u
lt err by skipp
i
ng tests
commit
|
commitdiff
|
tree
2002-07-29
jas
o
n
tests
updated
to
h
andle missing exe
b
etter
commit
|
commitdiff
|
tree
2002-07-29
jason
inher
i
t from W
r
apperBase
commit
|
commitdiff
|
tree
2002-07-29
jason
c
ode formatting
commit
|
commitdiff
|
tree
2002-07-29
ja
s
on
A
PI change
d
a little bit
w
ith
new parser
commit
|
commitdiff
|
tree
2002-07-29
jason
handle windo
w
s
e
xes
commit
|
commitdiff
|
tree
2002-07-29
jason
f
ix test cou
n
t
commit
|
commitdiff
|
tree
2002-07-29
jaso
n
u
s
e new PAML par
s
er
API
commit
|
commitdiff
|
tree
2002-07-27
jason
codem
l
->protml doc fi
x
es
commit
|
commitdiff
|
tree
2002-07-27
j
a
son
a
d
ded
a
d
d
i
t
ions of
.
exe f
o
r on
windows, al
l
ow alignm
e
nt
.
.
.
commit
|
commitdiff
|
tree
2002-07-27
j
a
son
bro
u
ght in line
with WrapperBase
commit
|
commitdiff
|
tree
2002-07-27
jaso
n
bro
u
ght
m
o
dule in-
l
ine
w
ith new Wrap
p
erBase
commit
|
commitdiff
|
tree
2002-07-27
jason
bump test count
commit
|
commitdiff
|
tree
2002-07-27
jas
o
n
copy
+
paste error
commit
|
commitdiff
|
tree
2002-07-27
jas
o
n
fix internal p
a
ram
e
t
e
r
name
commit
|
commitdiff
|
tree
2002-07-27
jason
added
ProtML wrapper - pa
r
t o
f
Molphy
packager for
.
.
.
commit
|
commitdiff
|
tree
2002-07-27
j
a
s
on
test
f
or
protml ru
n
n
ing
commit
|
commitdiff
|
tree
2002-07-25
jas
o
n
migrate from PA
M
LBase to Wra
p
pe
r
Base
commit
|
commitdiff
|
tree
2002-07-16
jason
print data to file
right away rather than ho
l
d
ing array
.
.
.
commit
|
commitdiff
|
tree
2002-07-16
j
a
son
don't
redirect to
/dev/null - mak
e
s
u
re quiet
really
.
.
.
commit
|
commitdiff
|
tree
2002-07-16
jason
more robust p
r
og
r
am finding
commit
|
commitdiff
|
tree
2002-07-09
jason
c
h
anged
t
o
use PAML template for
f
ind executable
i
nsated
.
.
.
commit
|
commitdiff
|
tree
2002-07-06
j
as
o
n
explicit
l
y closi
n
g some fileh
a
n
d
l
e
s appears to do a
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jason
tests find the mat and data f
i
le
n
ow
,
and
will skip
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jason
need
t
o tes
t
when peopl
e
run Makef
i
le
.
PL, otherwis
e
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jason
p
rompt user when Makefile
.
PL is run
commit
|
commitdiff
|
tree
2002-07-05
jason
updat
e
tes
t
count
commit
|
commitdiff
|
tree
2002-07-03
jason
m
a
kefile
commit
|
commitdiff
|
tree
2002-07-02
jason
added codeml data
commit
|
commitdiff
|
tree
2002-07-02
ja
s
on
r
emoved run wrappers tes
t
s
f
rom
core - th
e
y have be
e
n
.
.
.
commit
|
commitdiff
|
tree
2002-06-26
jas
o
n
r
e
a
d
me for
r
un
wrappers
commit
|
commitdiff
|
tree
2002-06-21
jason
testfile rename
d
commit
|
commitdiff
|
tree
2002-06-21
jason
remove debug copyfile
commit
|
commitdiff
|
tree
2002-06-21
jason
s
h
o
rten filename to a
v
oid pos
s
ible windows long
fi
l
e
n
ames
.
.
.
commit
|
commitdiff
|
tree
2002-06-19
jason
d
oc fix
commit
|
commitdiff
|
tree
2002-06-18
jason
u
s
e the dete
r
mined path to RP when at
t
em
p
ting to
f
ind
.
.
.
commit
|
commitdiff
|
tree
2002-06-17
jas
o
n
retur
n
th
e
values
a
s hash
of hashes as they are all
.
.
.
commit
|
commitdiff
|
tree
2002-06-17
jason
small doc twe
a
ks and ad
d
ed runnabl
e
synopsi
s
commit
|
commitdiff
|
tree
2002-06-17
jason
yn00 wrapper
f
o
r
P
A
ML
commit
|
commitdiff
|
tree
2002-06-15
ja
s
on
qui
e
ter tests u
n
less
B
IOP
E
RLDEBUG
e
nv v
a
riable is s
e
t
commit
|
commitdiff
|
tree
2002-06-14
jason
set verbose to
-
1
commit
|
commitdiff
|
tree
2002-06-14
j
a
s
on
PA
M
L package -- codeml wrappe
r
and t
e
st committe
d
commit
|
commitdiff
|
tree
2002-05-31
jaso
n
doc fix
commit
|
commitdiff
|
tree
2002-05-31
ja
s
on
handle
c
ase when P
H
YLIP is installed but not c
l
ustalw
commit
|
commitdiff
|
tree
2002-05-30
jason
h
andle some
weird boundary c
a
ses
commit
|
commitdiff
|
tree
2002-05-21
j
a
son
upd
a
t
e
some of th
e
docs
commit
|
commitdiff
|
tree
2002-05-21
jason
test value f
o
r
pro
t
dist
commit
|
commitdiff
|
tree
2002-04-22
jaso
n
fixes
t
o
remov
e
wa
r
nings
commit
|
commitdiff
|
tree
2002-04-22
j
a
son
fix warnings
commit
|
commitdiff
|
tree
2002-04-18
jason
POD
f
i
x
commit
|
commitdiff
|
tree
2002-03-22
jason
updated tests for
v
1
.
22 problems
o
n main
t
runk
commit
|
commitdiff
|
tree
2002-03-21
j
ason
sim
p
le align ha
s
overall perc
e
nt id method
commit
|
commitdiff
|
tree
2002-03-19
jason
cleanup
b
efore each run of
a
n
a
pplication
commit
|
commitdiff
|
tree
2002-03-15
jaso
n
merge from
b
r
anch
commit
|
commitdiff
|
tree
2002-03-15
jason
merg
e
cha
n
ges from branch
commit
|
commitdiff
|
tree
2002-03-15
j
as
o
n
updated to handle tests with Sear
c
hIO object returne
d
.
.
.
commit
|
commitdiff
|
tree
2002-03-15
jason
b
ette
r
synopsis and doc update
commit
|
commitdiff
|
tree
2002-03-14
j
ason
io cleanup ca
l
led
at outs
e
t
of
an ana
l
ys
e
s -- fr
o
m
.
.
.
commit
|
commitdiff
|
tree
2002-03-14
jason
merged
e
xe checking fro
m
branc
h
commit
|
commitdiff
|
tree
2002-03-14
jason
skip ni
c
ely, handle
c
ase
whe
r
e server is down
commit
|
commitdiff
|
tree
2002-03-11
j
a
so
n
u
s
e SearchIO not Too
l
s::Blast
commit
|
commitdiff
|
tree
2002-03-09
jason
turn of clu
s
talw
debugging
commit
|
commitdiff
|
tree
2002-03-05
jason
unli
n
k test file ou
t
put
commit
|
commitdiff
|
tree
2002-03-04
jason
add
e
d a
b
ility t
o
dump alignmen
t
s as well as sequences
.
.
.
commit
|
commitdiff
|
tree
2002-02-18
ja
s
on
added example do
c
u
m
entati
o
n to the POD
commit
|
commitdiff
|
tree
2002-02-18
jason
test for c
m
d lin
e
argument where value is a Bio::PrimarySeqI
.
.
.
commit
|
commitdiff
|
tree
2002-02-18
jas
o
n
h
andle c
m
d line arguments pointing
t
o
a Bio::PrimarySeqI
.
.
.
commit
|
commitdiff
|
tree
2002-02-06
ja
s
on
params should
b
e ap
p
en
d
ed n
o
t o
v
erwriting
commit
|
commitdiff
|
tree
2002-01-30
j
ason
verb
o
sity=-1 is same as quie
t
(
)
commit
|
commitdiff
|
tree
2002-01-11
jason
debug
m
essage n
o
w use
s
the debug method
commit
|
commitdiff
|
tree
2002-01-09
ja
s
on
wa
r
n
a
b
o
ut
not using old clus
t
alw
commit
|
commitdiff
|
tree
2002-01-09
jason
use the
u
p
d
a
ted
PRO
G
RAM exe
l
ocation inf
o
r
mation to
.
.
.
commit
|
commitdiff
|
tree
2002-01-09
jason
check to insure defined object before calli
n
g ISA
commit
|
commitdiff
|
tree
2001-12-14
jason
skip msg up
d
ated due to clu
s
tal
1
.
81 bug
commit
|
commitdiff
|
tree
2001-12-14
ja
s
on
nice m
e
ssage prin
t
ing wh
e
n blast is not runnable
commit
|
commitdiff
|
tree
2001-12-14
j
a
son
more qu
i
e
t warning
so test
s
are l
e
ss chatty
commit
|
commitdiff
|
tree
2001-12-14
jason
is
s
ue ni
c
e message w
h
e
n
skipping EMBOSS tests
commit
|
commitdiff
|
tree
2001-12-14
ja
s
o
n
skip can
print a
n
ice mess
a
g
e about why it ski
p
p
e
d
commit
|
commitdiff
|
tree
2001-12-14
ja
s
on
emboss factory
b
ehav
e
s
more quie
t
ly
when
E
M
B
OS
S
is
.
.
.
commit
|
commitdiff
|
tree
2001-11-19
jason
EM
B
OSS m
o
re ru
n
nab
l
e and w/ tests
commit
|
commitdiff
|
tree
2001-08-10
j
a
son
don't
have c
l
ustalw tests fai
l
for 0
.
9 release
commit
|
commitdiff
|
tree
2001-08-07
jason
d
ocum
e
ntati
o
n for retrieve_
b
l
ast
m
ethod
commit
|
commitdiff
|
tree
2001-06-15
j
as
o
n
minium identity scor
e
required ins
t
ead of hard va
l
ue
.
.
.
commit
|
commitdiff
|
tree
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