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default should be F3X4
2002-09-18
ja
s
on
de
f
au
l
t should
b
e F3X4
commit
|
commitdiff
|
tree
2002-09-18
jason
M
a
t
thew's Chang
e
s
commi
t
te
d
:
A
d
d
sup
p
ort to save_output
.
.
.
commit
|
commitdiff
|
tree
2002-09-18
j
a
s
o
n
handle e
x
e
apps
commit
|
commitdiff
|
tree
2002-09-05
ja
s
o
n
SAX
/
Sax
-> PerlSAX
commit
|
commitdiff
|
tree
2002-08-14
j
a
son
for building manifest
commit
|
commitdiff
|
tree
2002-08-14
jason
cosm
e
t
i
c code fix
commit
|
commitdiff
|
tree
2002-08-14
ja
s
on
descr
i
b
e
the
cu
r
r
ent state of
affair
commit
|
commitdiff
|
tree
2002-07-30
j
ason
s
kip tests
commit
|
commitdiff
|
tree
2002-07-29
jason
test f
i
le f
o
r
T
Co
f
f
e
e
commit
|
commitdiff
|
tree
2002-07-29
ja
s
on
who
o
ps,one more tim
e
, cleanup
t
e
mpfiles and
d
irs
commit
|
commitdiff
|
tree
2002-07-29
jaso
n
c
l
eanup of tempfiles work
s
commit
|
commitdiff
|
tree
2002-07-29
j
a
so
n
han
d
le bad
res
u
lt err by skipping tests
commit
|
commitdiff
|
tree
2002-07-29
jason
tests update
d
to
han
d
le m
i
s
s
ing ex
e
better
commit
|
commitdiff
|
tree
2002-07-29
j
a
son
i
nherit from Wrapp
e
rBas
e
commit
|
commitdiff
|
tree
2002-07-29
jason
code for
m
atting
commit
|
commitdiff
|
tree
2002-07-29
jason
API
c
hange
d
a
l
i
ttle bit with new p
a
rs
e
r
commit
|
commitdiff
|
tree
2002-07-29
ja
s
on
handle wi
n
dows exe
s
commit
|
commitdiff
|
tree
2002-07-29
jaso
n
f
ix test co
u
nt
commit
|
commitdiff
|
tree
2002-07-29
jason
u
s
e
new P
A
ML par
s
e
r API
commit
|
commitdiff
|
tree
2002-07-27
ja
s
on
codeml->
p
rotml doc
f
i
xes
commit
|
commitdiff
|
tree
2002-07-27
jason
add
e
d additi
o
ns of
.
ex
e
for o
n
windows, allow ali
g
nme
n
t
.
.
.
commit
|
commitdiff
|
tree
2002-07-27
jas
o
n
broug
h
t in line w
i
th WrapperBase
commit
|
commitdiff
|
tree
2002-07-27
jas
o
n
brou
g
ht m
o
dule in-line wi
t
h new Wr
a
pperBa
s
e
commit
|
commitdiff
|
tree
2002-07-27
j
a
s
on
b
ump tes
t
c
o
unt
commit
|
commitdiff
|
tree
2002-07-27
jason
c
o
py
+
pa
s
te er
r
or
commit
|
commitdiff
|
tree
2002-07-27
jason
fi
x
internal par
a
me
t
er name
commit
|
commitdiff
|
tree
2002-07-27
jaso
n
added
P
rotML wrap
p
er - part of Mo
l
phy
p
ack
a
ger
for
.
.
.
commit
|
commitdiff
|
tree
2002-07-27
jas
o
n
test
f
o
r pro
t
ml run
n
ing
commit
|
commitdiff
|
tree
2002-07-25
jason
m
i
g
rate from PAMLBase to WrapperBase
commit
|
commitdiff
|
tree
2002-07-16
j
a
son
prin
t
d
a
ta to
file right
a
w
ay rather than
h
olding
a
rr
a
y
.
.
.
commit
|
commitdiff
|
tree
2002-07-16
jason
don
'
t redire
c
t
to /dev/null
- m
a
ke sure qui
e
t really
.
.
.
commit
|
commitdiff
|
tree
2002-07-16
jason
more robus
t
program finding
commit
|
commitdiff
|
tree
2002-07-09
jason
changed to use P
A
M
L template for find
e
x
ec
u
table insated
.
.
.
commit
|
commitdiff
|
tree
2002-07-06
jason
e
xp
l
icitly closing some
f
ilehandl
e
s app
e
ars to do a
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
ja
s
o
n
tests find the mat
a
n
d d
a
ta file n
o
w, and wil
l
skip
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jason
need to test when people run Makefile
.
PL,
o
therwise
.
.
.
commit
|
commitdiff
|
tree
2002-07-05
jas
o
n
prompt user when Mak
e
file
.
PL is run
commit
|
commitdiff
|
tree
2002-07-05
j
a
son
u
pdate tes
t
count
commit
|
commitdiff
|
tree
2002-07-03
jason
m
a
k
efi
l
e
commit
|
commitdiff
|
tree
2002-07-02
j
ason
added
codeml
d
a
ta
commit
|
commitdiff
|
tree
2002-07-02
jaso
n
r
e
m
oved run w
r
a
p
per
s
t
e
s
ts from core - they
h
ave been
.
.
.
commit
|
commitdiff
|
tree
2002-06-26
j
a
so
n
readme for ru
n
w
r
appers
commit
|
commitdiff
|
tree
2002-06-21
jason
tes
t
file renamed
commit
|
commitdiff
|
tree
2002-06-21
jason
r
e
move
d
ebug copyf
i
le
commit
|
commitdiff
|
tree
2002-06-21
j
as
o
n
shorten filena
m
e to avoid p
o
ssib
l
e w
i
nd
o
ws l
o
ng fil
e
na
m
es
.
.
.
commit
|
commitdiff
|
tree
2002-06-19
j
a
s
on
doc fix
commit
|
commitdiff
|
tree
2002-06-18
jaso
n
u
se the determined p
a
th to RP when attempting to f
i
nd
.
.
.
commit
|
commitdiff
|
tree
2002-06-17
j
ason
r
eturn
the valu
e
s a
s
hash of ha
s
h
e
s as
th
e
y are all
.
.
.
commit
|
commitdiff
|
tree
2002-06-17
j
ason
small doc tweaks and added runnabl
e
synopsis
commit
|
commitdiff
|
tree
2002-06-17
jaso
n
yn
0
0 wrap
p
er for PAM
L
commit
|
commitdiff
|
tree
2002-06-15
jason
quiet
e
r tests unless BIO
P
ERLDEBU
G
env var
i
able is se
t
commit
|
commitdiff
|
tree
2002-06-14
jason
set verbose to -1
commit
|
commitdiff
|
tree
2002-06-14
j
a
s
on
PAML
p
ackage -
-
c
o
deml wrap
p
er
a
nd
t
est
c
o
mmitte
d
commit
|
commitdiff
|
tree
2002-05-31
jason
d
oc fix
commit
|
commitdiff
|
tree
2002-05-31
jason
ha
n
dle case wh
e
n PHYLI
P
is installed b
u
t n
o
t
clust
a
lw
commit
|
commitdiff
|
tree
2002-05-30
jas
o
n
h
and
l
e some weir
d
b
o
undary
cases
commit
|
commitdiff
|
tree
2002-05-21
jason
update som
e
of the docs
commit
|
commitdiff
|
tree
2002-05-21
j
a
son
t
est
value for protdist
commit
|
commitdiff
|
tree
2002-04-22
jason
f
i
xes to remo
v
e w
a
rnings
commit
|
commitdiff
|
tree
2002-04-22
j
as
o
n
fix warnings
commit
|
commitdiff
|
tree
2002-04-18
j
a
s
o
n
POD fix
commit
|
commitdiff
|
tree
2002-03-22
jason
updated tests for v
1
.
2
2 p
r
obl
e
ms
on ma
i
n t
r
u
n
k
commit
|
commitdiff
|
tree
2002-03-21
jason
simple
a
l
ig
n
h
as overall percent id m
e
t
hod
commit
|
commitdiff
|
tree
2002-03-19
ja
s
on
cleanup before
e
ach run of an applicatio
n
commit
|
commitdiff
|
tree
2002-03-15
jason
merge from branch
commit
|
commitdiff
|
tree
2002-03-15
jaso
n
m
e
r
g
e
changes fr
o
m branch
commit
|
commitdiff
|
tree
2002-03-15
jaso
n
u
p
d
a
ted to handle tests wit
h
Se
a
rc
h
IO obj
e
ct ret
u
rned
.
.
.
commit
|
commitdiff
|
tree
2002-03-15
jas
o
n
be
t
ter s
y
nopsis and d
o
c update
commit
|
commitdiff
|
tree
2002-03-14
jason
io cl
e
anup
c
a
lled at
outset of an anal
y
ses
-- from
.
.
.
commit
|
commitdiff
|
tree
2002-03-14
jaso
n
m
e
rged exe chec
k
ing from bra
n
ch
commit
|
commitdiff
|
tree
2002-03-14
j
ason
skip nicely, handle case
w
here server i
s
d
own
commit
|
commitdiff
|
tree
2002-03-11
jason
use Sea
r
chIO
not Tools::Blast
commit
|
commitdiff
|
tree
2002-03-09
jason
turn
o
f
clustalw debuggi
n
g
commit
|
commitdiff
|
tree
2002-03-05
jason
unlink
t
e
s
t f
i
l
e
output
commit
|
commitdiff
|
tree
2002-03-04
ja
s
on
added ability to dump align
m
ents as w
e
ll
as seq
u
ences
.
.
.
commit
|
commitdiff
|
tree
2002-02-18
j
ason
added example docu
m
e
n
tatio
n
to th
e
PO
D
commit
|
commitdiff
|
tree
2002-02-18
j
ason
test f
o
r cmd
line argument w
h
ere
v
a
l
u
e is a Bio::Primar
y
SeqI
.
.
.
commit
|
commitdiff
|
tree
2002-02-18
ja
s
on
handle cmd
l
i
ne argume
n
ts pointing to a
B
io::PrimarySeqI
.
.
.
commit
|
commitdiff
|
tree
2002-02-06
jason
params shoul
d
be appended not ov
e
rwriti
n
g
commit
|
commitdiff
|
tree
2002-01-30
jason
v
e
rbosi
t
y
=-1 is s
a
me as q
u
iet()
commit
|
commitdiff
|
tree
2002-01-11
jason
d
ebug message n
o
w
u
se
s
the debug method
commit
|
commitdiff
|
tree
2002-01-09
ja
s
o
n
warn
a
b
out no
t
using old clustalw
commit
|
commitdiff
|
tree
2002-01-09
jason
u
se t
h
e updated PROGRAM exe
l
oc
a
tion
info
r
mation to
.
.
.
commit
|
commitdiff
|
tree
2002-01-09
jason
c
h
eck to insure defined object befor
e
calling ISA
commit
|
commitdiff
|
tree
2001-12-14
jason
skip msg upda
t
e
d
d
u
e to
clustal
1
.
81 bug
commit
|
commitdiff
|
tree
2001-12-14
jason
nice me
s
sage printing whe
n
bl
a
s
t
is not runnable
commit
|
commitdiff
|
tree
2001-12-14
jason
more quie
t
warni
n
g so te
s
ts
are less c
h
atty
commit
|
commitdiff
|
tree
2001-12-14
jas
o
n
issue
nic
e
m
essage wh
e
n
s
kipp
i
n
g EMBOSS te
s
ts
commit
|
commitdiff
|
tree
2001-12-14
jason
sk
i
p
c
an print a
n
ice
m
e
s
sage abo
u
t why it skipped
commit
|
commitdiff
|
tree
2001-12-14
jason
emboss factory behaves
mo
r
e q
u
i
e
tl
y
when EMBOSS is
.
.
.
commit
|
commitdiff
|
tree
2001-11-19
jason
EMBO
S
S more
r
unnable and w/ test
s
commit
|
commitdiff
|
tree
2001-08-10
ja
s
on
don't have c
l
ustalw tests fail for 0
.
9 rele
a
se
commit
|
commitdiff
|
tree
2001-08-07
jason
d
o
cumenta
t
i
o
n
fo
r
retrieve_blast method
commit
|
commitdiff
|
tree
2001-06-15
jason
mi
n
ium iden
t
ity sc
o
r
e
re
q
uired instead
o
f hard valu
e
.
.
.
commit
|
commitdiff
|
tree
2001-06-14
jason
status set t
o
inv
a
lid o
n
a failed retrieval
commit
|
commitdiff
|
tree
2001-06-12
jason
using pr
i
vate
s
t
ate outsid
e
of class,
m
ust c
h
ange the
.
.
.
commit
|
commitdiff
|
tree
2001-04-30
jason
m
igrate
d
test data files to dir t/data
commit
|
commitdiff
|
tree
2001-04-16
jaso
n
Tests pas
s
even
w
hen IO::String
i
s not insta
l
l
ed
commit
|
commitdiff
|
tree
2001-04-09
jason
updated to use ncbi
B
l
ast
.
c
g
i
script rather t
h
an blast
.
cgi
commit
|
commitdiff
|
tree
2001-04-07
jason
updat
e
d num of tests
commit
|
commitdiff
|
tree
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